QTL Analysis - binary [ICI vs PBS]

workflowr

• Summary
• Checks
• Past versions

Last updated: 2022-04-08

Checks: 5 2

Knit directory: Serreze-T1D_Workflow/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

---

R Markdown file: uncommitted changes

The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20220210)

The command set.seed(20220210) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: absolute

Using absolute paths to the files within your workflowr project makes it difficult for you and others to run your code on a different machine. Change the absolute path(s) below to the suggested relative path(s) to make your code more reproducible.

absolute	relative
/Users/corneb/Documents/MyJax/CS/Projects/Serreze/qc/workflowr/Serreze-T1D_Workflow	.

Repository version: 2d6f369

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 2d6f369. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .DS_Store
    Ignored:    analysis/.DS_Store
    Ignored:    data/.DS_Store

Untracked files:
    Untracked:  analysis/0.1.1_preparing.data_bqc_5.batches.Rmd
    Untracked:  analysis/0.1_samples_batch_20220328.Rmd
    Untracked:  analysis/0.2_haplotype_comparison_bqc_5.batches_minprob.Rmd
    Untracked:  analysis/2.1_sample_bqc_5.batches.Rmd
    Untracked:  analysis/2.2.1_snp_qc_5.batches.Rmd
    Untracked:  analysis/2.2.1_snp_qc_5.batches_mis.Rmd
    Untracked:  analysis/2.2.1_snp_qc_5.batches_mis.Rmd.R
    Untracked:  analysis/2.4_preparing.data_aqc_5.batches.Rmd
    Untracked:  analysis/2.4_preparing.data_aqc_5.batches_mis.Rmd
    Untracked:  analysis/3.1_phenotype.qc_corrected_5.batches.Rmd
    Untracked:  analysis/3.1_phenotype.qc_corrected_5.batches_mis.Rmd
    Untracked:  analysis/3.1_phenotype.qc_corrected_5.batches_mis.Rmd.R
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_5.batches.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_5.batches_mis.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_snpsqc_5.batches.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_snpsqc_5.batches_mis.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_snpsqc_dis_no-x_updated_5.batches.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_snpsqc_dis_no-x_updated_5.batches_11.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_snpsqc_dis_no-x_updated_5.batches_mis.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_snpsqc_dis_no-x_updated_5.batches_mis_11.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_5.batches.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_5.batches_mis.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_5.batches.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_5.batches_1.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_5.batches_mis.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_5.batches_mis_1.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_5.batches.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_5.batches_1.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_5.batches_11.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_5.batches_mis.Rmd
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_5.batches_mis.Rmd.R
    Untracked:  analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_5.batches_mis_11.Rmd
    Untracked:  analysis/genotype.frequencies_ici.vs.eoi_5.batches.Rmd
    Untracked:  analysis/genotype.frequencies_ici.vs.eoi_5.batches_mis.Rmd
    Untracked:  analysis/genotype.frequencies_ici.vs.pbs_5.batches.Rmd
    Untracked:  analysis/genotype.frequencies_ici.vs.pbs_5.batches_mis.Rmd
    Untracked:  analysis/index_3.batches.Rmd
    Untracked:  analysis/index_4.batches.Rmd
    Untracked:  analysis/index_5.batches.Rmd
    Untracked:  analysis/index_5.batches_additional.Rmd
    Untracked:  analysis/index_5.batches_additional.Rmd.R
    Untracked:  data/GM_covar.csv
    Untracked:  data/GM_covar_BC312.csv
    Untracked:  data/bad_markers_all_4.batches.RData
    Untracked:  data/bad_markers_all_5.batches.RData
    Untracked:  data/blup_sub_chr10_lod.drop-1.5_5.batches.csv
    Untracked:  data/blup_sub_chr3_lod.drop-1.5.csv
    Untracked:  data/blup_sub_chr3_lod.drop-1.5_5.batches.csv
    Untracked:  data/blup_sub_chr4_lod.drop-1.5.csv
    Untracked:  data/blup_sub_chr4_lod.drop-1.5_5.batches.csv
    Untracked:  data/covar_cleaned_ici.vs.eoi.csv
    Untracked:  data/covar_cleaned_ici.vs.pbs.csv
    Untracked:  data/covar_corrected.cleaned_ici.vs.eoi.csv
    Untracked:  data/covar_corrected.cleaned_ici.vs.eoi1.csv
    Untracked:  data/covar_corrected.cleaned_ici.vs.eoi_5.batches.csv
    Untracked:  data/covar_corrected.cleaned_ici.vs.eoi_5.batches_mis.csv
    Untracked:  data/covar_corrected.cleaned_ici.vs.pbs.csv
    Untracked:  data/covar_corrected.cleaned_ici.vs.pbs1.csv
    Untracked:  data/covar_corrected.cleaned_ici.vs.pbs_5.batches.csv
    Untracked:  data/covar_corrected.cleaned_ici.vs.pbs_5.batches_mis.csv
    Untracked:  data/covar_corrected_ici.vs.eoi.csv
    Untracked:  data/covar_corrected_ici.vs.eoi1.csv
    Untracked:  data/covar_corrected_ici.vs.eoi_5.batches.csv
    Untracked:  data/covar_corrected_ici.vs.eoi_5.batches_mis.csv
    Untracked:  data/covar_corrected_ici.vs.pbs.csv
    Untracked:  data/covar_corrected_ici.vs.pbs1.csv
    Untracked:  data/covar_corrected_ici.vs.pbs_5.batches.csv
    Untracked:  data/covar_corrected_ici.vs.pbs_5.batches_mis.csv
    Untracked:  data/e.RData
    Untracked:  data/e_BC312.RData
    Untracked:  data/e_snpg_samqc_4.batches.RData
    Untracked:  data/e_snpg_samqc_4.batches_bc.RData
    Untracked:  data/e_snpg_samqc_5.batches.RData
    Untracked:  data/errors_ind_4.batches.RData
    Untracked:  data/errors_ind_4.batches_bc.RData
    Untracked:  data/errors_ind_5.batches.RData
    Untracked:  data/fitqtl_chr3.peak_chr4.peak_additive.txt
    Untracked:  data/fitqtl_chr3.peak_chr4.peak_interacting.txt
    Untracked:  data/fitqtl_chr3.peak_chr4.peak_sex_additive.txt
    Untracked:  data/fitqtl_chr3.peak_chr4.peak_sex_interacting.txt
    Untracked:  data/g2blup_effects.csv
    Untracked:  data/g2blup_effects.xlsx
    Untracked:  data/genes_chr10_lod.drop-1.5_5.batches.csv
    Untracked:  data/genes_chr3_lod.drop-1.5.csv
    Untracked:  data/genes_chr3_lod.drop-1.5_5.batches.csv
    Untracked:  data/genes_chr4_lod.drop-1.5.csv
    Untracked:  data/genetic_map.csv
    Untracked:  data/genetic_map_BC312.csv
    Untracked:  data/genotype_errors_marker_4.batches.RData
    Untracked:  data/genotype_errors_marker_5.batches.RData
    Untracked:  data/genotype_freq_marker_4.batches.RData
    Untracked:  data/genotype_freq_marker_5.batches.RData
    Untracked:  data/gm_allqc_4.batches.RData
    Untracked:  data/gm_allqc_5.batches.RData
    Untracked:  data/gm_allqc_5.batches_mis.RData
    Untracked:  data/gm_samqc_3.batches.RData
    Untracked:  data/gm_samqc_4.batches.RData
    Untracked:  data/gm_samqc_4.batches_bc.RData
    Untracked:  data/gm_samqc_5.batches.RData
    Untracked:  data/gm_serreze.192.RData
    Untracked:  data/gm_serreze.BC312.RData
    Untracked:  data/ici.vs.eoi_blup.full_chr-10_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-10_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-11_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-11_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-12_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-12_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-13_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-13_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-14_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-14_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-15_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-15_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-16_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-16_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-17_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-17_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-18_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-18_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-19_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-19_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-1_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-1_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-2_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-2_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-3_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-3_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-4_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-4_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-6_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-6_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-7_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-7_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-8_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-8_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-9_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-9_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-X_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.full_chr-X_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-10_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-10_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-10_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-10_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-10_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-10_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-10_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-11_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-11_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-11_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-11_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-11_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-11_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-11_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-12_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-12_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-12_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-12_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-12_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-12_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-12_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-13_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-13_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-13_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-13_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-13_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-13_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-13_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-14_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-14_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-14_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-14_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-14_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-14_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-15_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-15_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-15_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-15_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-15_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-16_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-16_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-16_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-16_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-16_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-16_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-17_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-17_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-17_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-17_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-17_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-17_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-18_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-18_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-18_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-18_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-18_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-18_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-19_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-19_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-19_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-19_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-19_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-19_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-1_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-1_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-1_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-1_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-1_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-1_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-1_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-2_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-2_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-2_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-2_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-2_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-2_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-2_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-3_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-3_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-3_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-3_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-3_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-3_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-3_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-4_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-4_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-4_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-4_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-4_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-4_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-4_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-5_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-6_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-6_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-6_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-6_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-6_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-6_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-6_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-7_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-7_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-7_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-7_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-7_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-7_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-7_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-8_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-8_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-8_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-8_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-8_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-8_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-8_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-9_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-9_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-9_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-9_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-9_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-9_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-9_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-X_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-X_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-X_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-X_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-X_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup.qc_chr-X_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-ICR4295_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-JAX00292499_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-JAX00292927_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-JAX00292927_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-JAX00292927_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-UNC18154330_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-UNC18195765_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-UNC18216614_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-UNC18240977_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-UNC18311938_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-UNC18856953_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-UNCHS028236_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-UNCHS028536_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-UNCJPD004316_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-10_peak.marker-UNCJPD009532_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-11_peak.marker-UNC19155926_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-11_peak.marker-UNC19481366_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-11_peak.marker-UNC19970181_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-11_peak.marker-UNC19970181_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-11_peak.marker-UNCJPD004792_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-12_peak.marker-ICR4497_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-12_peak.marker-ICR499_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-13_peak.marker-UNCHS036773_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-13_peak.marker-UNCHS036964_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-14_peak.marker-UNC24056202_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-14_peak.marker-UNC24056202_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-15_peak.marker-UNC26070435_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-17_peak.marker-UNCHS044241_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-17_peak.marker-UNCHS044241_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-17_peak.marker-UNCrs47191360_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-17_peak.marker-UNCrs47191360_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-18_peak.marker-UNCHS045344_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-19_peak.marker-UNCJPD007087_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-1_peak.marker-ICR010_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-1_peak.marker-ICR010_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-2_peak.marker-UNC4609527_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-2_peak.marker-UNC4609660_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-B6_rs31740628_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-ICR1269_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-ICR1338_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-ICR5325_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-ICR5347_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-ICR5348_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00104971_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00105059_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00105203_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00106957_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00106957_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00107930_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00107980_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00108068_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00108114_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00109750_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00189245_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00514662_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00517218_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00517674_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00517906_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00518418_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00518684_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00518911r_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00520122_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00524717_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00524828_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00525380_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00525709_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00527291_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00527587_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00529707_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00529707r_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00531601_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-JAX00532122_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4673471_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4681411_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4793677_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4799475_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4809586_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4813186_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4813186_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4820379_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4875653_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4909830_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4912288_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4914130_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4923398_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4924377_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4945186_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4947492_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4957168_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4957859_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4964062_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4979914_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4985064_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4990111_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC4991565_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5001723_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5008656_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5008656_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5042361_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5055259_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5076935_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5082757_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5083168_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5173293_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5182782_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5192582_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5193970_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5213888_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5240484_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5256922_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5266664_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5266711_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5267813_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5274554_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5277061_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5282259_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5287977_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5301460_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5321559_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5322455_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5328596_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5350384_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5354724_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5375208_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5384072_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5400314_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5433945_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5435874_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5454839_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5454839_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5466669_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5517972_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5522257_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5523265_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5532424_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5553882_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5572051_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5582753_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5589260_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5595555_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5623239_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5639830_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5645844_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5645844_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5680234_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5682314_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5725356_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5727351_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5734420_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5743257_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5751567_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5752623_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5776974_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5778977_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5788507_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5792468_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5794598_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5795561_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5802298_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5806628_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5808246_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5817478_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5836999_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5841501_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5847927_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNC5966417_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008129_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008173_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008182_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008193_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008209_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008215_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008219_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008231_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008235_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008242_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008253_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008256_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008259_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008271_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008286_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008286_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008311_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008317_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008372_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008379_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008410_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008415_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008431_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008511_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008609_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008614_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008649_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008651_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008656_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008723_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008802_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008803_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008808_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008815_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008815_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008834_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008838_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008914_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008928_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008948_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008959_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008973_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS008987_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009001_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009025_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009034_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009087_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009109_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009142_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009207_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009216_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009224_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009306_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009316_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009364_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009377_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009382_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009383_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009387_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009395_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009413_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009428_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009463_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009503_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009532_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009541_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009560_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCHS009574_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCJPD001170_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCJPD001198_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCJPD001276_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCJPD001315_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCJPD001355_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCJPD001373_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-3_peak.marker-UNCJPD001382_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNC6851205_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNC8250659_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNC8299912_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNC8300499_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNC8381981_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNC8436434_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNC8439633_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNC8530763_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNCHS012948_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNCHS012976_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNCHS013118_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNCHS013118_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNCHS013118_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNCHS013130_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNCHS013139_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-4_peak.marker-UNCHS013304_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-5_peak.marker-JAX00590770_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-5_peak.marker-UNC10044126_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-7_peak.marker-ICR1830_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-7_peak.marker-UNC13170794_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-7_peak.marker-UNCHS019480_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-7_peak.marker-cr31snv87_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-8_peak.marker-JAX00667121_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-8_peak.marker-UNC15430711_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-8_peak.marker-UNC15524531_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-9_peak.marker-UNC17203329_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-9_peak.marker-UNC17203597_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-9_peak.marker-UNCHS024593_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-X_peak.marker-UNC30627130_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-X_peak.marker-UNCHS048313_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-X_peak.marker-UNCHS048314_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_blup_sub_chr-X_peak.marker-UNCHS048314_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_additive_5.batches.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_additive_5.batches_mis.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_additive_snpsqc_dis_no-x_updated_5.batches.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_additive_snpsqc_dis_no-x_updated_5.batches_mis.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_interacting_5.batches.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_interacting_5.batches_mis.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_interacting_snpsqc_dis_no-x_updated_5.batches.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_interacting_snpsqc_dis_no-x_updated_5.batches_mis.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_sex_additive_5.batches.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_sex_additive_5.batches_mis.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_sex_additive_snpsqc_dis_no-x_updated_5.batches.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_sex_additive_snpsqc_dis_no-x_updated_5.batches_mis.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_sex_interacting_5.batches.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_sex_interacting_5.batches_mis.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_sex_interacting_snpsqc_dis_no-x_updated_5.batches.txt
    Untracked:  data/ici.vs.eoi_fitqtl_peaks_sex_interacting_snpsqc_dis_no-x_updated_5.batches_mis.mis.txt
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-ICR4295_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-JAX00292499_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-JAX00292927_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-JAX00292927_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-JAX00292927_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-UNC18154330_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-UNC18195765_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-UNC18216614_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-UNC18240977_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-UNC18311938_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-UNC18856953_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-UNCHS028236_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-UNCHS028536_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-UNCJPD004316_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-10_peak.marker-UNCJPD009532_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-11_peak.marker-UNC19155926_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-11_peak.marker-UNC19481366_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-11_peak.marker-UNC19970181_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-11_peak.marker-UNC19970181_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-11_peak.marker-UNCJPD004792_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-12_peak.marker-ICR4497_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-12_peak.marker-ICR499_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-13_peak.marker-UNCHS036773_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-13_peak.marker-UNCHS036964_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-14_peak.marker-UNC24056202_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-14_peak.marker-UNC24056202_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-15_peak.marker-UNC26070435_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-17_peak.marker-UNCHS044241_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-17_peak.marker-UNCHS044241_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-17_peak.marker-UNCrs47191360_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-17_peak.marker-UNCrs47191360_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-18_peak.marker-UNCHS045344_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-19_peak.marker-UNCJPD007087_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-1_peak.marker-ICR010_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-1_peak.marker-ICR010_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-2_peak.marker-UNC4609527_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-2_peak.marker-UNC4609660_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-B6_rs31740628_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-ICR1269_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-ICR1338_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-ICR5325_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-ICR5347_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-ICR5348_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00104971_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00105059_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00105203_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00106957_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00106957_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00107930_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00107980_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00108068_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00108114_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00109750_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00189245_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00514662_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00517218_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00517674_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00517906_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00518418_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00518684_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00518911r_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00520122_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00524717_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00524828_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00525380_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00525709_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00527291_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00527587_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00529707_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00529707r_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00531601_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-JAX00532122_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4673471_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4681411_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4793677_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4799475_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4809586_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4813186_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4813186_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4820379_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4875653_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4909830_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4912288_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4914130_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4923398_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4924377_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4945186_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4947492_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4957168_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4957859_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4964062_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4979914_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4985064_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4990111_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC4991565_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5001723_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5008656_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5008656_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5042361_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5055259_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5076935_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5082757_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5083168_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5173293_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5182782_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5192582_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5193970_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5213888_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5240484_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5256922_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5266664_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5266711_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5267813_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5274554_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5277061_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5282259_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5287977_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5301460_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5321559_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5322455_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5328596_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5350384_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5354724_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5375208_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5384072_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5400314_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5433945_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5435874_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5454839_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5454839_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5466669_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5517972_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5522257_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5523265_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5532424_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5553882_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5572051_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5582753_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5589260_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5595555_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5623239_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5639830_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5645844_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5645844_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5680234_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5682314_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5725356_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5727351_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5734420_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5743257_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5751567_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5752623_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5776974_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5778977_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5788507_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5792468_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5794598_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5795561_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5802298_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5806628_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5808246_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5817478_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5836999_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5841501_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5847927_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNC5966417_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008129_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008173_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008182_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008193_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008209_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008215_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008219_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008231_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008235_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008242_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008253_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008256_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008259_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008271_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008286_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008286_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008311_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008317_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008372_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008379_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008410_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008415_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008431_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008511_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008609_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008614_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008649_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008651_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008656_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008723_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008802_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008803_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008808_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008815_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008815_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008834_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008838_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008914_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008928_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008948_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008959_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008973_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS008987_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009001_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009025_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009034_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009087_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009109_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009142_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009207_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009216_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009224_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009306_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009316_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009364_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009377_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009382_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009383_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009387_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009395_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009413_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009428_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009463_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009503_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009532_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009541_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009560_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCHS009574_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCJPD001170_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCJPD001198_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCJPD001276_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCJPD001315_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCJPD001355_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCJPD001373_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-3_peak.marker-UNCJPD001382_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNC6851205_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNC8250659_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNC8299912_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNC8300499_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNC8381981_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNC8436434_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNC8439633_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNC8530763_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNCHS012948_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNCHS012976_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNCHS013118_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNCHS013118_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNCHS013118_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNCHS013130_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNCHS013139_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-4_peak.marker-UNCHS013304_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-5_peak.marker-JAX00590770_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-5_peak.marker-UNC10044126_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-7_peak.marker-ICR1830_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-7_peak.marker-UNC13170794_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-7_peak.marker-UNCHS019480_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.eoi_genes_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-7_peak.marker-cr31snv87_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-8_peak.marker-JAX00667121_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-8_peak.marker-UNC15430711_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-8_peak.marker-UNC15524531_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-9_peak.marker-UNC17203329_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-9_peak.marker-UNC17203597_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-9_peak.marker-UNCHS024593_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-X_peak.marker-UNC30627130_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-X_peak.marker-UNCHS048313_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-X_peak.marker-UNCHS048314_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_genes_chr-X_peak.marker-UNCHS048314_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_gm_qtl_5.batches.csv
    Untracked:  data/ici.vs.eoi_gm_qtl_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_gm_qtl_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_gm_qtl_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_gm_qtl_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.eoi_gm_qtl_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.geno.freq.removed_geno.ratio.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.geno.freq.removed_geno.ratio_5.batches.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.geno.freq.removed_geno.ratio_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_5.batches.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.probs.freq.removed_geno.ratio.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.probs.freq.removed_geno.ratio_5.batches.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.probs.freq.removed_geno.ratio_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_5.batches.csv
    Untracked:  data/ici.vs.eoi_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_sample.genos_marker.freq_low.geno.freq.removed.csv
    Untracked:  data/ici.vs.eoi_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed.csv
    Untracked:  data/ici.vs.eoi_sample.genos_marker.freq_low.probs.freq.removed.csv
    Untracked:  data/ici.vs.eoi_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv
    Untracked:  data/ici.vs.eoi_scanone_5.batches.Rdata
    Untracked:  data/ici.vs.eoi_scanone_5.batches_mis.Rdata
    Untracked:  data/ici.vs.eoi_scanone_snpsqc_5.batches.Rdata
    Untracked:  data/ici.vs.eoi_scanone_snpsqc_5.batches_mis.Rdata
    Untracked:  data/ici.vs.eoi_scanone_snpsqc_dis_no-x_updated_5.batches.Rdata
    Untracked:  data/ici.vs.pbs_bad.markers_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-10_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-10_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-10_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-10_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-10_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-11_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-11_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-11_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-11_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-11_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-12_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-12_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-12_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-12_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-12_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-13_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-13_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-13_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-13_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-13_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-14_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-14_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-14_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-14_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-14_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-15_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-15_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-15_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-15_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-15_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-16_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-16_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-16_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-16_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-16_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-17_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-17_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-17_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-17_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-17_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-18_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-18_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-18_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-18_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-18_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-19_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-19_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-19_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-19_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-19_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-1_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-1_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-1_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-1_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-1_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-2_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-2_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-2_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-2_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-2_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-3_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-3_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-3_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-3_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-3_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-4_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-4_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-4_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-4_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-4_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-5_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-6_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-6_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-6_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-6_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-6_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-7_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-7_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-7_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-7_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-7_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-8_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-8_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-8_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-8_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-8_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-9_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-9_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-9_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-9_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-9_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-X_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-X_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-X_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-X_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.full_chr-X_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-10_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-10_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-10_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-10_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-10_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-10_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-10_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-10_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-11_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-11_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-11_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-11_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-11_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-11_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-11_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-11_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-12_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-12_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-12_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-12_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-12_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-12_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-12_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-12_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-13_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-13_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-13_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-13_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-13_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-13_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-13_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-13_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-14_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-14_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-14_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-14_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-14_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-14_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-14_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-15_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-15_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-15_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-15_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-15_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-16_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-16_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-16_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-16_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-16_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-16_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-16_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-17_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-17_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-17_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-17_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-17_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-18_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-18_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-18_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-18_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-18_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-18_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-18_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-19_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-19_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-19_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-19_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-19_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-19_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-19_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-1_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-1_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-1_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-1_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-1_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-1_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-1_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-1_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-2_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-2_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-2_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-2_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-2_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-2_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-2_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-2_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-3_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-3_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-3_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-3_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-3_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-3_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-3_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-3_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-4_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-4_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-4_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-4_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-4_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-4_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-4_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-4_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-5_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-5_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-6_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-6_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-6_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-6_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-6_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-6_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-6_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-6_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-7_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-7_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-7_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-7_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-7_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-7_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-7_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-7_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-8_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-8_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-8_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-8_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-8_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-8_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-8_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-8_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-9_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-9_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-9_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-9_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-9_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-9_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-9_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-9_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-X_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-X_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-X_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-X_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-X_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-X_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup.qc_chr-X_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-10_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-10_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-10_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-10_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-10_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-11_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-11_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-11_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-11_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-11_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-12_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-12_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-12_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-12_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-12_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-13_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-13_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-13_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-13_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-13_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-14_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-14_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-14_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-14_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-14_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-15_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-15_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-15_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-16_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-16_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-16_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-16_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-16_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-17_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-17_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-17_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-18_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-18_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-18_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-18_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-18_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-19_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-19_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-19_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-19_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-19_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-1_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-1_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-1_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-1_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-1_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-2_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-2_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-2_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-2_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-2_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-3_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-3_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-3_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-3_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-3_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-4_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-4_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-4_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-4_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-4_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-5_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-5_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-5_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-5_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-5_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-6_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-6_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-6_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-6_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-6_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-7_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-7_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-7_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-7_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-7_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-8_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-8_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-8_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-8_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-8_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-9_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-9_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-9_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-9_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-9_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-X_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-X_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-X_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_chr-X_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_blup_chr-X_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_blup_sub_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_genes_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_5.batches.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio_5.batches.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_5.batches.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_5.batches.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_5.batches.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv
    Untracked:  data/ici.vs.pbs_scanone_5.batches.Rdata
    Untracked:  data/ici.vs.pbs_scanone_5.batches_mis.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_5.batches.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_5.batches_mis.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_dis_no-x_updated_5.batches.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_dis_no-x_updated_5.batches_mis.Rdata
    Untracked:  data/percent_missing_id_3.batches.RData
    Untracked:  data/percent_missing_id_4.batches.RData
    Untracked:  data/percent_missing_id_4.batches_bc.RData
    Untracked:  data/percent_missing_id_5.batches.RData
    Untracked:  data/percent_missing_marker_4.batches.RData
    Untracked:  data/percent_missing_marker_5.batches.RData
    Untracked:  data/pheno.csv
    Untracked:  data/pheno_BC312.csv
    Untracked:  data/physical_map.csv
    Untracked:  data/physical_map_BC312.csv
    Untracked:  data/qc_info_bad_sample_3.batches.RData
    Untracked:  data/qc_info_bad_sample_4.batches.RData
    Untracked:  data/qc_info_bad_sample_4.batches_bc.RData
    Untracked:  data/qc_info_bad_sample_5.batches.RData
    Untracked:  data/remaining.markers_geno.freq.xlsx
    Untracked:  data/sample_geno.csv
    Untracked:  data/sample_geno_AHB_BC312.csv
    Untracked:  data/sample_geno_bc.csv
    Untracked:  data/sample_geno_bc_BC312.csv
    Untracked:  data/serreze_probs.rds
    Untracked:  data/serreze_probs_BC312.rds
    Untracked:  data/serreze_probs_allqc.rds
    Untracked:  data/serreze_probs_allqc_5.batches.rds
    Untracked:  data/serreze_probs_allqc_5.batches_mis.rds
    Untracked:  data/summary.cg_3.batches.RData
    Untracked:  data/summary.cg_4.batches.RData
    Untracked:  data/summary.cg_4.batches_bc.RData
    Untracked:  data/summary.cg_5.batches.RData
    Untracked:  output/Percent_missing_genotype_data_5.batches.pdf
    Untracked:  output/Percent_missing_genotype_data_per_marker_5.batches.pdf
    Untracked:  output/Proportion_matching_genotypes_before_removal_of_bad_samples_5.batches.pdf
    Untracked:  output/genotype_error_marker_5.batches.pdf
    Untracked:  output/genotype_frequency_marker_5.batches.pdf

Unstaged changes:
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_snpsqc_dis_no-x_updated.Rmd
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

---

There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.

---

Loading Data

We will load the data and subset indivials out that are in the groups of interest. We will create a binary phenotype from this (PBS ==0, ICI == 1).

load("data/gm_allqc_5.batches.RData")

#gm_allqc
gm=gm_allqc
gm

Object of class cross2 (crosstype "bc")

Total individuals              308
No. genotyped individuals      308
No. phenotyped individuals     308
No. with both geno & pheno     308

No. phenotypes                   1
No. covariates                   6
No. phenotype covariates         0

No. chromosomes                 20
Total markers                34537

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 1300 1549 1578 1257  935 
  17   18   19    X 
 501  913 1014 4532 

#pr <- readRDS("data/serreze_probs_allqc_5.batches.rds")
#pr <- readRDS("data/serreze_probs.rds")

##extracting animals with ici and pbs group status
miceinfo <- gm$covar[gm$covar$group == "PBS" | gm$covar$group == "ICI",]
table(miceinfo$group)

ICI PBS 
104  34 

mice.ids <- rownames(miceinfo)

gm <- gm[mice.ids]
gm

Object of class cross2 (crosstype "bc")

Total individuals              138
No. genotyped individuals      138
No. phenotyped individuals     138
No. with both geno & pheno     138

No. phenotypes                   1
No. covariates                   6
No. phenotype covariates         0

No. chromosomes                 20
Total markers                34537

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 1300 1549 1578 1257  935 
  17   18   19    X 
 501  913 1014 4532 

#pr.qc <- pr
#for (i in 1:20){pr.qc[[i]] = pr.qc[[i]][mice.ids,,]}

#bin_pheno <- NULL
#bin_pheno$PBS <- ifelse(gm$covar$group == "PBS", 1, 0)
#bin_pheno$ICI <- ifelse(gm$covar$group == "ICI", 1, 0)
#bin_pheno <- as.data.frame(bin_pheno)
#rownames(bin_pheno) <- rownames(gm$covar)

gm$covar$ICI.vs.PBS <- ifelse(gm$covar$group == "PBS", 0, 1)
gm.full <- gm

##removing problmetic marker

gm <- drop_markers(gm, "UNCHS013106")

markers <- marker_names(gm)
gmapdf <- read.csv("/Users/corneb/Documents/MyJax/CS/Projects/Serreze/haplotype.reconstruction/output_5.batches/genetic_map.csv")
pmapdf <- read.csv("/Users/corneb/Documents/MyJax/CS/Projects/Serreze/haplotype.reconstruction/output_5.batches/physical_map.csv")
#mapdf <- merge(gmapdf,pmapdf, by=c("marker","chr"), all=T)
#rownames(mapdf) <- mapdf$marker
#mapdf <- mapdf[markers,]
#names(mapdf) <- c('marker','chr','gmapdf','pmapdf')
#mapdfnd <- mapdf[!duplicated(mapdf[c(2:3)]),]

pr.qc <- calc_genoprob(gm)

gm

Object of class cross2 (crosstype "bc")

Total individuals              138
No. genotyped individuals      138
No. phenotyped individuals     138
No. with both geno & pheno     138

No. phenotypes                   1
No. covariates                   7
No. phenotype covariates         0

No. chromosomes                 20
Total markers                34537

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 1300 1549 1578 1257  935 
  17   18   19    X 
 501  913 1014 4532 

Genome-wide scan

For each of the phenotype analyzed, permutations were used for each model to obtain genome-wide LOD significance threshold for p < 0.01, p < 0.05, p < 0.10, respectively, separately for X and automsomes (A).

The table shows the estimated significance thresholds from permutation test.

We also looked at the kinship to see how correlated each sample is. Kinship values between pairs of samples range between 0 (no relationship) and 1.0 (completely identical). The darker the colour the more indentical the pairs are.

Xcovar <- get_x_covar(gm)
#addcovar = model.matrix(~Sex, data = covars)[,-1]

#K <- calc_kinship(pr.qc, type = "loco")
#heatmap(K[[1]])
#K.overall <- calc_kinship(pr.qc, type = "overall")
#heatmap(K.overall)
kinship <- calc_kinship(pr.qc)
heatmap(kinship)

#operm <- scan1perm(pr.qc, gm$covar$phenos, Xcovar=Xcovar, n_perm=2000)
#operm <- scan1perm(pr.qc, gm$covar$phenos, addcovar = addcovar, n_perm=2000)
#operm <- scan1perm(pr.qc, gm$covar$phenos, n_perm=2000)
operm <- scan1perm(pr.qc, gm$covar["ICI.vs.PBS"], model="binary", n_perm=10, perm_Xsp=TRUE, chr_lengths=chr_lengths(gm$gmap))

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))
names(summary_table) <- c("autosomes","X")
summary_table$significance.level <- rownames(summary_table)

rownames(summary_table) <- NULL

summary_table[c(3,1:2)] %>%
  kable(escape = F,align = c("ccc")) %>%
  kable_styling("striped", full_width = T) %>%
  column_spec(1, bold=TRUE)

significance.level	autosomes	X
0.01	3.750644	4.755759
0.05	3.487279	4.075399
0.1	3.157251	3.185710

The figures below show QTL maps for each phenotype

out <- scan1(pr.qc, gm$covar["ICI.vs.PBS"], Xcovar=Xcovar, model="binary")

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))

plot_lod<-function(out,map){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- 11 # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " [positions in cM] \n(using same scale as eoi  vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm, alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()
  }
}

plot_lod(out,gm$gmap)

LOD peaks

The table below shows QTL peaks associated with the phenotype. We use the 95% threshold from the permutations to find peaks.

Centimorgan (cM)

peaks <- find_peaks(out, gm$gmap, threshold=summary(operm,alpha=0.05)$A, thresholdX = summary(operm,alpha=0.05)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks$marker <- find_marker(gm$gmap, chr=peaks$chr,pos=peaks$pos)
names(peaks)[2] <- c("phenotype")
peaks <- peaks[-1]

rownames(peaks) <- NULL
print(kable(peaks, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

#plot only peak chromosomes

plot_lod_chr<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

    
    ymx <- 11
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in cM]\n(using same scale as eoi vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

  }
}


for(i in unique(peaks$chr)){
#for (i in 1:nrow(peaks)){
  #plot_lod_chr(out,gm$gmap, peaks$chr[i])
  plot_lod_chr(out,gm$gmap, i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.05) level of 3.4872786076933 [autosomes]/4.07539954214614 [x-chromosome]”

Megabase (MB)

print("peaks in MB positions")

[1] “peaks in MB positions”

peaks_mba <- find_peaks(out, gm$pmap, threshold=summary(operm,alpha=0.05)$A, thresholdX = summary(operm,alpha=0.05)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks_mba$marker <- find_marker(gm$pmap, chr=peaks_mba$chr,pos=peaks_mba$pos)
names(peaks_mba)[2] <- c("phenotype")
peaks_mba <- peaks_mba[-1]

#peaks_mbl <- list()
##corresponding info in Mb
#for(i in 1:nrow(peaks)){
#  #lodindex <- peaks$lodindex[i]
#  phenotype <- peaks$phenotype[i]
#  chr <- as.character(peaks$chr[i])
#  lod <- peaks$lod[i]
#  mark <- peaks$marker[i]
#  pos <- mapdf[mapdf$marker==mark,]$pmapdf
#  ci_lo <- mapdfnd$pmapdf[which(mapdfnd$gmapdf == peaks$ci_lo[i] & mapdfnd$chr == peaks$chr[i])]
#  ci_hi <- mapdfnd$pmapdf[which(mapdfnd$gmapdf == peaks$ci_hi[i] & mapdfnd$chr == peaks$chr[i])]
#  peaks_mb=as.data.frame(cbind(phenotype, chr, pos, lod, ci_lo, ci_hi, mark))
#  names(peaks_mb)[7] <- c("marker")
#  peaks_mbl[[i]] <- peaks_mb
#}
#peaks_mba2 <- do.call(rbind, peaks_mbl)
#peaks_mba2 <- as.data.frame(peaks_mba)
#peaks_mba[,c("chr", "pos", "lod", "ci_lo", "ci_hi")] <- sapply(peaks_mba[,c("chr", "pos", "lod", "ci_lo", "ci_hi")], as.numeric)

rownames(peaks_mba) <- NULL

print(kable(peaks_mba, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

plot_lod_chr_mb<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in MB]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

    ymx <- 11
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in MB]\n(using same scale as eoi vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')


  }
}

for(i in unique(peaks_mba$chr)){
#for (i in 1:nrow(peaks_mba)){
  #plot_lod_chr_mb(out,gm$pmap, peaks_mba$chr[i])
  plot_lod_chr_mb(out,gm$pmap,i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.05) level of 3.4872786076933 [autosomes]/4.07539954214614 [x-chromosome]”

QTL effects

For each peak LOD location we give a list of gene

query_variants <- create_variant_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/cc_variants.sqlite")
query_genes <- create_gene_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/mouse_genes_mgi.sqlite")

if(nrow(peaks) >0){
for (i in 1:nrow(peaks)){
#for (i in 1:1){
  #Plot 1
  g <- maxmarg(pr.qc, gm$gmap, chr=peaks$chr[i], pos=peaks$pos[i], return_char=TRUE)
  #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/","qtl_effect_", i, ".png"))
  #par(mar=c(4.1, 4.1, 1.5, 0.6))
  plot_pxg(g, gm$covar[,peaks$phenotype[i]], ylab=peaks$phenotype[i], sort=FALSE)
  title(main = paste0("chr: ", chr=peaks$chr[i], "pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," )"), line=0.2)
  ##dev.off()

  chr = peaks$chr[i]

# Plot 2
  pr_sub <- pull_genoprobint(pr.qc, gm$gmap, chr, c(peaks$ci_lo[i], peaks$ci_hi[i]))
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar)
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], Xcovar=Xcovar)
  #coeff <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  #coeff_sub <- scan1coef(pr_sub[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  blup <- scan1blup(pr.qc[,chr], gm$covar[peaks$phenotype[i]])
  blup_sub <- scan1blup(pr_sub[,chr], gm$covar[peaks$phenotype[i]])

  write.csv(as.data.frame(blup_sub), paste0("data/ici.vs.pbs_blup_sub_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches.csv"), quote=F)

  #plot_coef(coeff, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i]," [scan1coeff; positions in cM])")
  #     )

  #plot_coef(coeff_sub, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i],"; 1.5 LOD drop interval [scan1coeff; positions in cM] ) ")
  #     )


  plot_coef(blup, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i], "pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," [scan1blup; positions in cM])")
       )

  plot_coef(blup_sub, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i], "pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i],"; 1.5 LOD drop interval [scan1blup; positions in cM])")
       )


 # Plot 3
  #c2effB <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary", contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  #c2effBb <- scan1blup(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]],Xcovar=Xcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  #plot(c2effB, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  #plot(c2effBb, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  ##last_coef <- unclass(c2effB)[nrow(c2effB),2:3] # last two coefficients
  ##for(t in seq(along=last_coef))
  ##  axis(side=4, at=last_coef[t], names(last_coef)[t], tick=FALSE)


  #Table 1
  chr = peaks_mba$chr[i]
  start=as.numeric(peaks_mba$ci_lo[i])
  end=as.numeric(peaks_mba$ci_hi[i])

  genesgss = query_genes(chr, start, end)

  write.csv(genesgss, file=paste0("data/ici.vs.pbs_genes_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches.csv"), quote=F)

  rownames(genesgss) <- NULL
  genesgss$strand_old = genesgss$strand
  genesgss$strand[genesgss$strand=="+"] <- "positive"
  genesgss$strand[genesgss$strand=="-"] <- "negative"

  #genesgss <- 
  #table <- 
  #genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")] %>%
  #kable(escape = F,align = c("ccccccccccc")) %>%
  #kable_styling("striped", full_width = T) #%>% 
  #cat #%>%
  #column_spec(1, bold=TRUE)
#
  #print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], escape = F,align = c("ccccccccccc")))

  print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], "html") %>% kable_styling("striped", full_width = T))

  #table
  

}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.05) level of 3.4872786076933 [autosomes]/4.07539954214614 [x-chromosome]”

R/qtl

scanone

gm

Object of class cross2 (crosstype "bc")

Total individuals              138
No. genotyped individuals      138
No. phenotyped individuals     138
No. with both geno & pheno     138

No. phenotypes                   1
No. covariates                   7
No. phenotype covariates         0

No. chromosomes                 20
Total markers                34537

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 1300 1549 1578 1257  935 
  17   18   19    X 
 501  913 1014 4532 

#detach("package:qtl2", unload=TRUE)
#library(qtl)

cross <- qtl::read.cross("csv", file = "data/ici.vs.pbs_gm_qtl_5.batches.csv",alleles=c("A","B"))

 --Read the following data:
     138  individuals
     34537  markers
     3  phenotypes
 --Cross type: bc 

cross <- qtl::jittermap(cross)

summary(cross)

    Backcross

    No. individuals:    138 

    No. phenotypes:     3 
    Percent phenotyped: 100 100 100 

    No. chromosomes:    20 
        Autosomes:      1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 
        X chr:          X 

    Total markers:      34537 
    No. markers:        2643 2629 1857 1890 1774 1941 1672 1627 1878 1176 1871 
                        1300 1549 1578 1257 935 501 913 1014 4532 
    Percent genotyped:  99.4 
    Genotypes (%):    
          Autosomes:    AA:59.8  AB:40.2 
       X chromosome:    AA:95.9  AB:4.1  

cross.probs <- qtl::calc.genoprob(cross)

print("method == hk")

[1] "method == hk"

scanone.hk <-qtl::scanone(cross.probs, pheno.col="ICI.vs.PBS" , model="binary", method="hk")
operm.hk <- qtl::scanone(cross.probs, method = "hk", pheno.col="ICI.vs.PBS", n.perm = 10, perm.Xsp = TRUE, model="binary", verbose=FALSE)
plot(operm.hk)

print(summary(operm.hk, alpha=c(0.01,  0.05, 0.1)))

Autosome LOD thresholds (10 permutations)
     lod
1%  4.25
5%  3.74
10% 3.12

X chromosome LOD thresholds (181 permutations)
     lod
1%  3.31
5%  3.29
10% 3.27

#plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "steelblue")  
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

ymx <- maxlod(out) # overall maximum LOD score
plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "slateblue", ylim=c(0, ymx+0.5))
title(main = paste0(colnames(out), " [positions in cM]"))
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

ymx <- 11
plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "slateblue", ylim=c(0, ymx+0.5))
title(main = paste0(colnames(out), " [positions in cM]\n(using same scale as eoi vs. ici for easier comparison)"))
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

print(as.data.frame(summary(scanone.hk, perms=operm.hk, pvalues=TRUE, format="allpeaks")))

            chr       pos       lod      pval
UNC163443     1  4.774084 1.3742470 1.0000000
UNCHS005128   2 35.575604 1.3907437 1.0000000
UNC5265500    3 23.363432 1.5065527 1.0000000
UNCHS012528   4 53.470029 1.6634197 0.9119556
JAX00591328   5 52.052170 1.7146365 0.7193229
UNC10846758   6 14.425266 0.7729249 1.0000000
UNC13819275   7 69.998488 0.9313595 1.0000000
UNCHS023364   8 35.540889 1.5630473 1.0000000
UNC17298291   9 73.251870 1.5592674 1.0000000
UNCHS029562  10 77.099163 1.0768916 1.0000000
UNCHS031091  11 40.242075 1.0460115 1.0000000
ICR4362      12  8.289190 1.4861271 1.0000000
UNC22620355  13 28.179586 1.1779989 1.0000000
UNCHS038071  14 22.374371 1.2540580 1.0000000
UNC25285746  15 12.031164 1.0160042 1.0000000
UNCHS042473  16 25.979308 1.0343994 1.0000000
UNCHS044622  17 31.021132 1.7849879 0.6197628
UNC29628452  18 51.369806 0.7730316 1.0000000
UNC29893228  19  8.029065 1.6198742 1.0000000
XiB2          X 45.699832 1.8700869 0.9902556

print("all peaks with a p-value less or equal to 0.05 (suggestive)")

[1] "all peaks with a p-value less or equal to 0.05 (suggestive)"

print(as.data.frame(summary(scanone.hk, perms=operm.hk, alpha=0.05, pvalues=TRUE, format="allpeaks")))

[1] chr pos lod
<0 rows> (or 0-length row.names)

#print("method == ehk")

#scanone.ehk <-qtl::scanone(cross.probs, pheno.col="ICI.vs.PBS" , model="binary", method="ehk")
#operm.ehk <- qtl::scanone(cross.probs, method = "ehk", pheno.col="ICI.vs.PBS", n.perm = 1000, perm.Xsp = TRUE, model="binary", verbose=FALSE)
#plot(operm.ehk)
#print(summary(operm.ehk, alpha=c(0.01,  0.05, 0.1)))

#plot(scanone.ehk, bandcol = "grey90",lty=1, cex=1, col = "steelblue")  
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.01, col = 'blue')
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.05, col = 'red')
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.1, col = 'purple')

#print(as.data.frame(summary(scanone.ehk)))
#print(as.data.frame(summary(scanone.ehk, perms=operm.ehk, alpha=0.05, pvalues=TRUE, format="allpeaks")))

Session information

R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] abind_1.4-5       qtl2_0.22         reshape2_1.4.4    ggplot2_3.3.5    
 [5] tibble_3.1.2      psych_2.0.7       readxl_1.3.1      cluster_2.1.0    
 [9] dplyr_1.0.8       optparse_1.6.6    rhdf5_2.28.1      mclust_5.4.6     
[13] tidyr_1.0.2       data.table_1.14.0 knitr_1.33        kableExtra_1.1.0 
[17] workflowr_1.6.2  

loaded via a namespace (and not attached):
 [1] httr_1.4.1        bit64_4.0.5       viridisLite_0.4.0 assertthat_0.2.1 
 [5] highr_0.9         blob_1.2.1        cellranger_1.1.0  yaml_2.2.1       
 [9] pillar_1.6.1      RSQLite_2.2.7     backports_1.2.1   lattice_0.20-38  
[13] glue_1.4.2        digest_0.6.27     promises_1.1.0    rvest_0.3.5      
[17] colorspace_2.0-2  htmltools_0.5.1.1 httpuv_1.5.2      plyr_1.8.6       
[21] pkgconfig_2.0.3   purrr_0.3.4       scales_1.1.1      webshot_0.5.2    
[25] qtl_1.46-2        getopt_1.20.3     later_1.0.0       git2r_0.26.1     
[29] generics_0.0.2    ellipsis_0.3.2    cachem_1.0.5      withr_2.4.2      
[33] cli_3.0.0         mnormt_1.5-7      magrittr_2.0.1    crayon_1.4.1     
[37] memoise_2.0.0     evaluate_0.14     fs_1.4.1          fansi_0.5.0      
[41] nlme_3.1-142      xml2_1.3.1        tools_3.6.2       hms_0.5.3        
[45] lifecycle_1.0.1   stringr_1.4.0     Rhdf5lib_1.6.3    munsell_0.5.0    
[49] compiler_3.6.2    rlang_1.0.2       grid_3.6.2        rstudioapi_0.13  
[53] rmarkdown_2.1     gtable_0.3.0      DBI_1.1.1         R6_2.5.0         
[57] fastmap_1.1.0     bit_4.0.4         utf8_1.2.1        rprojroot_1.3-2  
[61] readr_1.3.1       stringi_1.7.2     parallel_3.6.2    Rcpp_1.0.7       
[65] vctrs_0.3.8       tidyselect_1.1.2  xfun_0.24