Last updated: 2023-04-13

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Knit directory: Serreze-T1D_Workflow/

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    Untracked:  data/sample_geno_AHB_7.batches_myo_orig.id.csv
    Untracked:  data/sample_geno_bc_4.batches_myo.csv
    Untracked:  data/sample_geno_bc_7.batches_myo.csv
    Untracked:  data/sample_geno_bc_7.batches_myo_orig.id.csv
    Untracked:  data/serreze_probs_4.batches_myo.rds
    Untracked:  data/serreze_probs_7.batches_myo.rds
    Untracked:  data/serreze_probs_allqc_4.batches_myo.rds
    Untracked:  data/serreze_probs_allqc_4.batches_myo_mis.rds
    Untracked:  data/serreze_probs_allqc_7.batches_myo.rds
    Untracked:  data/serreze_probs_allqc_7.batches_myo_mis.rds
    Untracked:  data/summary.cg_4.batches_myo.RData
    Untracked:  data/summary.cg_7.batches_myo.RData
    Untracked:  output/Percent_missing_genotype_data_4.batches_myo.pdf
    Untracked:  output/Percent_missing_genotype_data_7.batches_myo.pdf
    Untracked:  output/Percent_missing_genotype_data_per_marker_4.batches_myo.pdf
    Untracked:  output/Percent_missing_genotype_data_per_marker_7.batches_myo.pdf
    Untracked:  output/Proportion_matching_genotypes_before_removal_of_bad_samples_4.batches_myo.pdf
    Untracked:  output/Proportion_matching_genotypes_before_removal_of_bad_samples_7.batches_myo.pdf
    Untracked:  output/genotype_error_marker_4.batches_myo.pdf
    Untracked:  output/genotype_error_marker_7.batches_myo.pdf
    Untracked:  output/genotype_frequency_marker_4.batches_myo.pdf
    Untracked:  output/genotype_frequency_marker_7.batches_myo.pdf

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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Preparing Files

load("data/gm_allqc_7.batches_myo.RData")

gm_allqc
Object of class cross2 (crosstype "bc")

Total individuals              357
No. genotyped individuals      357
No. phenotyped individuals     357
No. with both geno & pheno     357

No. phenotypes                   1
No. covariates                  11
No. phenotype covariates         0

No. chromosomes                 20
Total markers                32660

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
2482 2412 1742 1772 1648 1842 1541 1517 1769 1092 1754 1230 1441 1505 1128  842 
  17   18   19    X 
 655  820  945 4523 
pr <- calc_genoprob(gm_allqc)

saveRDS(pr, file = "data/serreze_probs_allqc_7.batches_myo.rds")

sessionInfo()
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] abind_1.4-5       qtl2_0.30         reshape2_1.4.4    ggplot2_3.4.0    
 [5] tibble_3.1.8      psych_2.2.9       readxl_1.4.1      cluster_2.1.4    
 [9] dplyr_1.0.10      optparse_1.7.3    rhdf5_2.40.0      mclust_6.0.0     
[13] tidyr_1.2.1       data.table_1.14.6 knitr_1.41        kableExtra_1.3.4 
[17] workflowr_1.7.0  

loaded via a namespace (and not attached):
 [1] httr_1.4.4         sass_0.4.4         bit64_4.0.5        jsonlite_1.8.4    
 [5] viridisLite_0.4.1  bslib_0.4.1        assertthat_0.2.1   getPass_0.2-2     
 [9] highr_0.9          blob_1.2.3         cellranger_1.1.0   yaml_2.3.6        
[13] pillar_1.8.1       RSQLite_2.2.19     lattice_0.20-45    glue_1.6.2        
[17] digest_0.6.30      promises_1.2.0.1   rvest_1.0.3        colorspace_2.0-3  
[21] htmltools_0.5.3    httpuv_1.6.6       plyr_1.8.8         pkgconfig_2.0.3   
[25] purrr_0.3.5        scales_1.2.1       webshot_0.5.4      processx_3.8.0    
[29] svglite_2.1.0      whisker_0.4.1      getopt_1.20.3      later_1.3.0       
[33] git2r_0.30.1       generics_0.1.3     cachem_1.0.6       withr_2.5.0       
[37] cli_3.4.1          mnormt_2.1.1       magrittr_2.0.3     memoise_2.0.1     
[41] evaluate_0.18      ps_1.7.2           fs_1.5.2           fansi_1.0.3       
[45] nlme_3.1-161       xml2_1.3.3         tools_4.2.2        lifecycle_1.0.3   
[49] stringr_1.5.0      Rhdf5lib_1.18.2    munsell_0.5.0      callr_3.7.3       
[53] compiler_4.2.2     jquerylib_0.1.4    systemfonts_1.0.4  rlang_1.0.6       
[57] grid_4.2.2         rhdf5filters_1.8.0 rstudioapi_0.14    rmarkdown_2.18    
[61] gtable_0.3.1       DBI_1.1.3          R6_2.5.1           bit_4.0.5         
[65] fastmap_1.1.0      utf8_1.2.2         rprojroot_2.0.3    stringi_1.7.8     
[69] parallel_4.2.2     Rcpp_1.0.9         vctrs_0.5.1        tidyselect_1.2.0  
[73] xfun_0.35