Serreze Workflow - 7 batches/6 groups

workflowr

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Last updated: 2023-04-17

Checks: 6 1

Knit directory: Serreze-T1D_Workflow/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. 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

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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: relative

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Repository version: 52c77a4

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 52c77a4. 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:

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    Untracked:  data/gm_allqc_7.batches_myo.RData
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    Untracked:  data/gm_samqc_4.batches_myo.RData
    Untracked:  data/gm_samqc_7.batches_myo.RData
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    Untracked:  data/gm_serreze_bc_7.batches_myo.RData
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/het-ici.vs.het-pbs_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/het-ici.vs.het-pbs_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/het-ici.vs.het-pbs_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/het-ici.vs.het-pbs_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/het-ici.vs.het-pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/het-ici.vs.het-pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/het-ici.vs.het-pbs_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/het-ici.vs.het-pbs_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/het-ici.vs.het-pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/het-ici.vs.het-pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo.csv
    Untracked:  data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-10_peak.marker-UNC18343990_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-10_peak.marker-UNC18343990_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-11_peak.marker-UNC20070077_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-11_peak.marker-UNC20070077_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-12_peak.marker-UNC21652584_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-12_peak.marker-UNC21652584_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-13_peak.marker-UNCHS036579_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-13_peak.marker-UNCHS036579_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-14_peak.marker-UNCHS037782_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-14_peak.marker-UNCHS037782_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-15_peak.marker-UNC26069905_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-15_peak.marker-UNCHS041223_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-16_peak.marker-JAX00070117_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-16_peak.marker-JAX00070117_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-17_peak.marker-UNC28542319_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-17_peak.marker-UNCJPD006670_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-18_peak.marker-UNC28776739_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-18_peak.marker-UNCHS045594_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-19_peak.marker-UNC30414168_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-19_peak.marker-UNC30426276_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-1_peak.marker-UNC2031646_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-1_peak.marker-UNCHS003700_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-2_peak.marker-ICR5131_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-2_peak.marker-UNCHS006420_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-3_peak.marker-UNC5667757_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-3_peak.marker-UNC5667757_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-4_peak.marker-UNC6759992_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-4_peak.marker-UNC6765178_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-5_peak.marker-UNC9889957_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-5_peak.marker-UNC9900273_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-6_peak.marker-UNC10800126_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-6_peak.marker-UNC10832076_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-7_peak.marker-UNCHS020903_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-7_peak.marker-UNCHS021163_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-8_peak.marker-UNC15471847_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-8_peak.marker-UNC15548888_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-9_peak.marker-UNC16231874_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-9_peak.marker-UNC16231874_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-X_peak.marker-UNCHS049472_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-X_peak.marker-UNCHS049472_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-10_peak.marker-UNC18343990_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-10_peak.marker-UNC18343990_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-11_peak.marker-UNC20070077_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-11_peak.marker-UNC20070077_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-12_peak.marker-UNC21652584_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-12_peak.marker-UNC21652584_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-13_peak.marker-UNCHS036579_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-13_peak.marker-UNCHS036579_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-14_peak.marker-UNCHS037782_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-14_peak.marker-UNCHS037782_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-15_peak.marker-UNC26069905_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-15_peak.marker-UNCHS041223_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-16_peak.marker-JAX00070117_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-16_peak.marker-JAX00070117_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-17_peak.marker-UNC28542319_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-17_peak.marker-UNCJPD006670_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-18_peak.marker-UNC28776739_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-18_peak.marker-UNCHS045594_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-19_peak.marker-UNC30414168_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-19_peak.marker-UNC30426276_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-1_peak.marker-UNC2031646_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-1_peak.marker-UNCHS003700_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-2_peak.marker-ICR5131_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-2_peak.marker-UNCHS006420_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-3_peak.marker-UNC5667757_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-3_peak.marker-UNC5667757_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-4_peak.marker-UNC6759992_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-4_peak.marker-UNC6765178_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-5_peak.marker-UNC9889957_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-5_peak.marker-UNC9900273_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-6_peak.marker-UNC10800126_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-6_peak.marker-UNC10832076_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-7_peak.marker-UNCHS020903_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-7_peak.marker-UNCHS021163_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-8_peak.marker-UNC15471847_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-8_peak.marker-UNC15548888_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-9_peak.marker-UNC16231874_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-9_peak.marker-UNC16231874_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-X_peak.marker-UNCHS049472_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-X_peak.marker-UNCHS049472_lod.drop-1.5_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_age.of.onset_pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_age.of.onset_pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/mean.differences_group_pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/mean.differences_group_pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_gm_qtl_snpsqc_dis_no-x_updated_7.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_7.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_7.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.probs.freq.removed_7.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_7.batches_myo.csv
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Unstaged changes:
    Modified:   analysis/index_7.batches_myo.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.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index_7.batches_myo.Rmd) and HTML (docs/index_7.batches_myo.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	efe4c01	Belinda Cornes	2023-04-17	myocarditis html files 7 batches
Rmd	732a0a5	Belinda Cornes	2023-04-17	myocarditis Rmd files 7 batches

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Neogen Files At A Glance [Total Samples: 366]

• Samples: The_Jackson_Lab_Serreze_MURGIGV01_20220729
  • Total Samples: 48
• Samples: The_Jackson_Lab_Serreze_MURGIGV01_20220826
  • Total Samples: 12
• Samples: The_Jackson_Lab_Serreze_MURGIGV01_20221006
  • Total Samples: 85
• Samples: The_Jackson_Lab_Serreze_MURGIGV01_20221116
  • Total Samples: 72
• Samples: The_Jackson_Lab_Serreze_MURGIGV01_20230124
  • Total Samples: 36
• Samples: The_Jackson_Lab_Serreze_MURGIGV01_20230225
  • Total Samples: 95
• Samples: The_Jackson_Lab_Serreze_MURGIGV01_20230313
  • Total Samples: 18 [Note: Sample D249-PBS-EOI, also appears in the previous group submitted in Feb 2023]
• Preparing files for QC/Haplotype Phasing

Haplotype Phasing

• minimum probability set for estimation of genotypes

1. Experiment Design

abbreviations for strains:	AB: het; AA: hom
type of cross:	Backcross
number of mice phenotyped:	366
total number of mice phenotypes:	2 [1 binary/1 quantiative]
phenotypes:	myocarditis status/group [binary] & age of onset [continuous]
number of mice:	366
number of markers:	137302
covariates:	sex [F: 344; M: 22] ; and others depending on samples used in analysis

2. Genotype QC

• Step 1: Sample QC
• Step 2: SNP QC(removing monomorphic, genotype error & missing markers)
• Step 3: Preparing Files for QTL Analysis
• Step 4: Identifying additional disproportionate markers within each sample set
  • ICI Sick vs ICI EOI
  • ICI vs PBS
  • ICI Myocarditis Yes vs ICI Myocarditis No
  • PBS Myocarditis Yes vs PBS Myocarditis No
  • Myocarditis Yes vs Myocarditis No
  • Hetero: ICI vs PBS
  • Hetero: ICI Myocarditis Yes vs ICI Myocarditis No

3. Phenotype QC

continous phenotypes (age of onset) [not necessary for current analysis]

• Corrected Phenotypes
  • all comparisons

4. QTL Analysis

binary phenotpe

I reran these a couple of different ways as I am not sure why its difficult to get any results

** ANALYSIS ONE **

1. removed additional low frequency markers as well as disproportionate markers (identified in Step 2.4) within each sample set
2. no X covariate (ie. Xcovar); using sex as a covariate
3. no kinship included as r/qtl2 does not allow for the inclusion of a kinship matrix in this type of model
4. For each model run, permutations (1000) 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)

• ICI Sick vs ICI EOI
• ICI vs PBS
• ICI Myocarditis Yes vs ICI Myocarditis No
• PBS Myocarditis Yes vs PBS Myocarditis No
• Myocarditis Yes vs Myocarditis No
• Hetero: ICI vs PBS
• Hetero: ICI Myocarditis Yes vs ICI Myocarditis No

** ANALYSIS TWO **

The same as above but removing sex as a covariate (not sure if confounding might be an issue)

• ICI Sick vs ICI EOI
• ICI vs PBS
• ICI Myocarditis Yes vs ICI Myocarditis No
• PBS Myocarditis Yes vs PBS Myocarditis No
• Myocarditis Yes vs Myocarditis No
• Hetero: ICI vs PBS
• Hetero: ICI Myocarditis Yes vs ICI Myocarditis No

** ANALYSIS THREE **

same as analysis one but this time kept disproportionate markers (removed low frequency markers). That is, kept sex as covariate.

• ICI Sick vs ICI EOI
• ICI vs PBS
• ICI Myocarditis Yes vs ICI Myocarditis No
• PBS Myocarditis Yes vs PBS Myocarditis No
• Myocarditis Yes vs Myocarditis No
• Hetero: ICI vs PBS
• Hetero: ICI Myocarditis Yes vs ICI Myocarditis No

** ANALYSIS FOUR **

same as analysis three but removed sex.

• ICI Sick vs ICI EOI
• ICI vs PBS
• ICI Myocarditis Yes vs ICI Myocarditis No
• PBS Myocarditis Yes vs PBS Myocarditis No
• Myocarditis Yes vs Myocarditis No
• Hetero: ICI vs PBS
• Hetero: ICI Myocarditis Yes vs ICI Myocarditis No

** ANALYSIS FIVE **

suggested by Vivek P.:

1. map binary phenotype (drug treatment - ICI vs. PBS)
   • Murine MHC KO Status & clinical phenotype as an additive covariates
   • Qn: is there a genetic difference between drug treatment groups, regardless of clinical phenotype, KO or Myocarditis Status?
2. map binary phenotype (clinical phenotype - SICK vs. EOI)
   • Murine MHC KO Status & drug treatment as an additive covariates
   • Qn: is there a genetic difference between clinical phenotype samples, regardless of drug treatment, KO or Myocarditis Status?
3. map binary phenotype (clinical phenotype - SICK vs. EOI within each drug treatment)
   • Murine MHC KO Status & drug treatment as an additive covariates
   • Qn: is there a genetic difference between clinical phenotype samples, regardless of KO or Myocarditis Status?

5. Power Analysis

Using ANALYSIS ONE

• ICI Sick vs ICI EOI
• ICI vs PBS
• ICI Myocarditis Yes vs ICI Myocarditis No
• PBS Myocarditis Yes vs PBS Myocarditis No
• Myocarditis Yes vs Myocarditis No
• Hetero: ICI vs PBS
• Hetero: ICI Myocarditis Yes vs ICI Myocarditis No

Session information

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] ggrepel_0.9.2     qtlcharts_0.16    qtl2_0.30         broman_0.80      
 [5] ggplot2_3.4.0     tibble_3.1.8      readxl_1.4.1      cluster_2.1.4    
 [9] dplyr_1.0.10      optparse_1.7.3    mclust_6.0.0      tidyr_1.2.1      
[13] data.table_1.14.6 knitr_1.42        kableExtra_1.3.4  workflowr_1.7.0  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9        svglite_2.1.0     getPass_0.2-2     ps_1.7.2         
 [5] assertthat_0.2.1  rprojroot_2.0.3   digest_0.6.31     utf8_1.2.2       
 [9] R6_2.5.1          cellranger_1.1.0  RSQLite_2.2.19    evaluate_0.20    
[13] httr_1.4.4        pillar_1.8.1      rlang_1.1.0       rstudioapi_0.14  
[17] blob_1.2.3        whisker_0.4.1     callr_3.7.3       jquerylib_0.1.4  
[21] rmarkdown_2.21.2  qtl_1.54          webshot_0.5.4     stringr_1.5.0    
[25] bit_4.0.5         munsell_0.5.0     compiler_4.2.2    httpuv_1.6.6     
[29] xfun_0.38         pkgconfig_2.0.3   systemfonts_1.0.4 htmltools_0.5.5  
[33] tidyselect_1.2.0  fansi_1.0.3       viridisLite_0.4.1 withr_2.5.0      
[37] later_1.3.0       grid_4.2.2        jsonlite_1.8.4    gtable_0.3.1     
[41] lifecycle_1.0.3   DBI_1.1.3         git2r_0.30.1      magrittr_2.0.3   
[45] scales_1.2.1      cli_3.6.1         stringi_1.7.12    cachem_1.0.7     
[49] fs_1.6.1          promises_1.2.0.1  getopt_1.20.3     xml2_1.3.3       
[53] bslib_0.4.2       generics_0.1.3    vctrs_0.6.1       tools_4.2.2      
[57] bit64_4.0.5       glue_1.6.2        purrr_0.3.5       parallel_4.2.2   
[61] processx_3.8.0    fastmap_1.1.1     yaml_2.3.7        colorspace_2.0-3 
[65] rvest_1.0.3       memoise_2.0.1     sass_0.4.5