Last updated: 2023-01-24
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.
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.
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.
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.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
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 c9fc66b. 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
Untracked files:
Untracked: analysis/0.1.1_preparing.data_bqc_4.batches_myo.Rmd
Untracked: analysis/0.1.1_preparing.data_bqc_4.batches_myo.Rmd.R
Untracked: analysis/0.1_samples_batch_20220729.Rmd
Untracked: analysis/0.1_samples_batch_20220729.Rmd.R
Untracked: analysis/0.1_samples_batch_20220826.Rmd
Untracked: analysis/0.1_samples_batch_20220826.Rmd.R
Untracked: analysis/0.1_samples_batch_20221006.Rmd
Untracked: analysis/0.1_samples_batch_20221006.Rmd.R
Untracked: analysis/0.1_samples_batch_20221116.Rmd
Untracked: analysis/0.1_samples_batch_20221116.Rmd.R
Untracked: analysis/0.2_haplotype_comparison_bqc_4.batches_myo_minprob.Rmd
Untracked: analysis/0.2_haplotype_comparison_bqc_4.batches_myo_minprob.Rmd.R
Untracked: analysis/2.1_sample_bqc_4.batches_myo.Rmd
Untracked: analysis/2.1_sample_bqc_4.batches_myo.Rmd.R
Untracked: analysis/2.2.1_snp_qc_4.batches_myo.Rmd
Untracked: analysis/2.2.1_snp_qc_4.batches_myo.Rmd.R
Untracked: analysis/2.2.1_snp_qc_4.batches_myo_mis.Rmd
Untracked: analysis/2.2.1_snp_qc_4.batches_myo_mis.Rmd.R
Untracked: analysis/2.4_preparing.data_aqc_4.batches_myo.Rmd
Untracked: analysis/2.4_preparing.data_aqc_4.batches_myo.Rmd.R
Untracked: analysis/2.4_preparing.data_aqc_4.batches_myo_mis.Rmd
Untracked: analysis/2.4_preparing.data_aqc_4.batches_myo_mis.Rmd.R
Untracked: analysis/3.1_phenotype.qc_corrected_4.batches_myo.Rmd
Untracked: analysis/3.1_phenotype.qc_corrected_4.batches_myo.Rmd.R
Untracked: analysis/3.1_phenotype.qc_corrected_4.batches_myo_mis.Rmd
Untracked: analysis/3.1_phenotype.qc_corrected_4.batches_myo_mis.Rmd.R
Untracked: analysis/4.1.1_qtl.analysis_binary_het-ici-myo-yes.vs.het-ici-myo-no_snpsqc_dis_no-x_updated_4.batches_myo.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_het-ici-myo-yes.vs.het-ici-myo-no_snpsqc_dis_no-x_updated_4.batches_myo.Rmd.R
Untracked: analysis/4.1.1_qtl.analysis_binary_het-ici-myo-yes.vs.het-ici-myo-no_snpsqc_dis_no-x_updated_4.batches_myo_mis.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_het-ici.vs.het-pbs_snpsqc_dis_no-x_updated_4.batches_myo.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_het-ici.vs.het-pbs_snpsqc_dis_no-x_updated_4.batches_myo.Rmd.R
Untracked: analysis/4.1.1_qtl.analysis_binary_het-ici.vs.het-pbs_snpsqc_dis_no-x_updated_4.batches_myo_mis.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_ici-myo-yes.vs.ici-myo-no_snpsqc_dis_no-x_updated_4.batches_myo.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_ici-myo-yes.vs.ici-myo-no_snpsqc_dis_no-x_updated_4.batches_myo.Rmd.R
Untracked: analysis/4.1.1_qtl.analysis_binary_ici-myo-yes.vs.ici-myo-no_snpsqc_dis_no-x_updated_4.batches_myo_mis.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_ici-sick.vs.ici-eoi_snpsqc_dis_no-x_updated_4.batches_myo.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_ici-sick.vs.ici-eoi_snpsqc_dis_no-x_updated_4.batches_myo.Rmd.R
Untracked: analysis/4.1.1_qtl.analysis_binary_ici-sick.vs.ici-eoi_snpsqc_dis_no-x_updated_4.batches_myo_mis.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_4.batches_myo.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_4.batches_myo.Rmd.R
Untracked: analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_4.batches_myo_mis.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_4.batches_myo_mis.Rmd.R
Untracked: analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated_4.batches_myo_mis1.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_myo-yes.vs.myo-no_snpsqc_dis_no-x_updated_4.batches_myo.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_myo-yes.vs.myo-no_snpsqc_dis_no-x_updated_4.batches_myo.Rmd.R
Untracked: analysis/4.1.1_qtl.analysis_binary_myo-yes.vs.myo-no_snpsqc_dis_no-x_updated_4.batches_myo_mis.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_pbs-myo-yes.vs.pbs-myo-no_snpsqc_dis_no-x_updated_4.batches_myo.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_pbs-myo-yes.vs.pbs-myo-no_snpsqc_dis_no-x_updated_4.batches_myo.Rmd.R
Untracked: analysis/4.1.1_qtl.analysis_binary_pbs-myo-yes.vs.pbs-myo-no_snpsqc_dis_no-x_updated_4.batches_myo_mis.Rmd
Untracked: analysis/4.1.1_qtl.analysis_binary_pbs-myo-yes.vs.pbs-myo-no_snpsqc_dis_no-x_updated_4.batches_myo_misRmd.Rmd
Untracked: analysis/genotype.frequencies_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo.Rmd
Untracked: analysis/genotype.frequencies_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo.Rmd.R
Untracked: analysis/genotype.frequencies_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo_mis.Rmd
Untracked: analysis/genotype.frequencies_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo_mis.Rmd.R
Untracked: analysis/genotype.frequencies_het-ici.vs.het-pbs_4.batches_myo.Rmd
Untracked: analysis/genotype.frequencies_het-ici.vs.het-pbs_4.batches_myo.Rmd.R
Untracked: analysis/genotype.frequencies_het-ici.vs.het-pbs_4.batches_myo_mis.Rmd
Untracked: analysis/genotype.frequencies_het-ici.vs.het-pbs_4.batches_myo_mis.Rmd.R
Untracked: analysis/genotype.frequencies_ici-myo-yes.vs.ici-myo-no_4.batches_myo.Rmd
Untracked: analysis/genotype.frequencies_ici-myo-yes.vs.ici-myo-no_4.batches_myo.Rmd.R
Untracked: analysis/genotype.frequencies_ici-myo-yes.vs.ici-myo-no_4.batches_myo_mis.Rmd
Untracked: analysis/genotype.frequencies_ici-myo-yes.vs.ici-myo-no_4.batches_myo_mis.Rmd.R
Untracked: analysis/genotype.frequencies_ici-sick.vs.ici-eoi_4.batches_myo.Rmd
Untracked: analysis/genotype.frequencies_ici-sick.vs.ici-eoi_4.batches_myo.Rmd.R
Untracked: analysis/genotype.frequencies_ici-sick.vs.ici-eoi_4.batches_myo_mis.Rmd
Untracked: analysis/genotype.frequencies_ici-sick.vs.ici-eoi_4.batches_myo_mis.Rmd.R
Untracked: analysis/genotype.frequencies_ici.vs.pbs_4.batches_myo.Rmd
Untracked: analysis/genotype.frequencies_ici.vs.pbs_4.batches_myo.Rmd.R
Untracked: analysis/genotype.frequencies_ici.vs.pbs_4.batches_myo_mis.Rmd
Untracked: analysis/genotype.frequencies_ici.vs.pbs_4.batches_myo_mis.Rmd.R
Untracked: analysis/genotype.frequencies_myo-yes.vs.myo-no_4.batches_myo.Rmd
Untracked: analysis/genotype.frequencies_myo-yes.vs.myo-no_4.batches_myo.Rmd.R
Untracked: analysis/genotype.frequencies_myo-yes.vs.myo-no_4.batches_myo_mis.Rmd
Untracked: analysis/genotype.frequencies_myo-yes.vs.myo-no_4.batches_myo_mis.Rmd.R
Untracked: analysis/genotype.frequencies_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo.Rmd
Untracked: analysis/genotype.frequencies_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo.Rmd.R
Untracked: analysis/genotype.frequencies_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo_mis.Rmd
Untracked: analysis/genotype.frequencies_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo_mis.Rmd.R
Untracked: analysis/index_4.batches_myo.Rmd
Untracked: analysis/index_4.batches_myo.Rmd.R
Untracked: analysis/power.analysis_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo.Rmd
Untracked: analysis/power.analysis_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo.Rmd.R
Untracked: analysis/power.analysis_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo_mis.Rmd
Untracked: analysis/power.analysis_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo_mis.Rmd.R
Untracked: analysis/power.analysis_het-ici.vs.het-pbs_4.batches_myo.Rmd
Untracked: analysis/power.analysis_het-ici.vs.het-pbs_4.batches_myo.Rmd.R
Untracked: analysis/power.analysis_het-ici.vs.het-pbs_4.batches_myo_mis.Rmd
Untracked: analysis/power.analysis_het-ici.vs.het-pbs_4.batches_myo_mis.Rmd.R
Untracked: analysis/power.analysis_ici-myo-yes.vs.ici-myo-no_4.batches_myo.Rmd
Untracked: analysis/power.analysis_ici-myo-yes.vs.ici-myo-no_4.batches_myo.Rmd.R
Untracked: analysis/power.analysis_ici-myo-yes.vs.ici-myo-no_4.batches_myo_mis.Rmd
Untracked: analysis/power.analysis_ici-myo-yes.vs.ici-myo-no_4.batches_myo_mis.Rmd.R
Untracked: analysis/power.analysis_ici-sick.vs.ici-eoi_4.batches_myo.Rmd
Untracked: analysis/power.analysis_ici-sick.vs.ici-eoi_4.batches_myo.Rmd.R
Untracked: analysis/power.analysis_ici-sick.vs.ici-eoi_4.batches_myo_mis.Rmd
Untracked: analysis/power.analysis_ici-sick.vs.ici-eoi_4.batches_myo_mis.Rmd.R
Untracked: analysis/power.analysis_ici.vs.pbs_4.batches_myo.R
Untracked: analysis/power.analysis_ici.vs.pbs_4.batches_myo.Rmd
Untracked: analysis/power.analysis_ici.vs.pbs_4.batches_myo.Rmd.R
Untracked: analysis/power.analysis_ici.vs.pbs_4.batches_myo_mis.Rmd
Untracked: analysis/power.analysis_ici.vs.pbs_4.batches_myo_mis.Rmd.R
Untracked: analysis/power.analysis_myo-yes.vs.myo-no_4.batches_myo.Rmd
Untracked: analysis/power.analysis_myo-yes.vs.myo-no_4.batches_myo.Rmd.R
Untracked: analysis/power.analysis_myo-yes.vs.myo-no_4.batches_myo_mis.Rmd
Untracked: analysis/power.analysis_myo-yes.vs.myo-no_4.batches_myo_mis.Rmd.R
Untracked: analysis/power.analysis_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo copy.Rmd.R
Untracked: analysis/power.analysis_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo.Rmd
Untracked: analysis/power.analysis_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo.Rmd.R
Untracked: analysis/power.analysis_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo_mis.Rmd
Untracked: analysis/power.analysis_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo_mis.Rmd.R
Untracked: data copy/
Untracked: data/GM_covar_4.batches_myo.csv
Untracked: data/bad_markers_all_4.batches_myo.RData
Untracked: data/covar_corrected.cleaned_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo.csv
Untracked: data/covar_corrected.cleaned_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo_mis.csv
Untracked: data/covar_corrected.cleaned_het-ici.vs.het-pbs_4.batches_myo.csv
Untracked: data/covar_corrected.cleaned_het-ici.vs.het-pbs_4.batches_myo_mis.csv
Untracked: data/covar_corrected.cleaned_ici-myo-yes.vs.ici-myo-no_4.batches_myo.csv
Untracked: data/covar_corrected.cleaned_ici-myo-yes.vs.ici-myo-no_4.batches_myo_mis.csv
Untracked: data/covar_corrected.cleaned_ici-sick.vs.ici-eoi_4.batches_myo.csv
Untracked: data/covar_corrected.cleaned_ici-sick.vs.ici-eoi_4.batches_myo_mis.csv
Untracked: data/covar_corrected.cleaned_ici.vs.pbs_4.batches_myo.csv
Untracked: data/covar_corrected.cleaned_ici.vs.pbs_4.batches_myo_mis.csv
Untracked: data/covar_corrected.cleaned_myo-yes.vs.myo-no_4.batches_myo.csv
Untracked: data/covar_corrected.cleaned_myo-yes.vs.myo-no_4.batches_myo_mis.csv
Untracked: data/covar_corrected.cleaned_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo.csv
Untracked: data/covar_corrected.cleaned_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo_mis.csv
Untracked: data/covar_corrected_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo.csv
Untracked: data/covar_corrected_het-ici-myo-yes.vs.het-ici-myo-no_4.batches_myo_mis.csv
Untracked: data/covar_corrected_het-ici.vs.het-pbs_4.batches_myo.csv
Untracked: data/covar_corrected_het-ici.vs.het-pbs_4.batches_myo_mis.csv
Untracked: data/covar_corrected_ici-myo-yes.vs.ici-myo-no_4.batches_myo.csv
Untracked: data/covar_corrected_ici-myo-yes.vs.ici-myo-no_4.batches_myo_mis.csv
Untracked: data/covar_corrected_ici-sick.vs.ici-eoi_4.batches_myo.csv
Untracked: data/covar_corrected_ici-sick.vs.ici-eoi_4.batches_myo_mis.csv
Untracked: data/covar_corrected_ici.vs.pbs_4.batches_myo.csv
Untracked: data/covar_corrected_ici.vs.pbs_4.batches_myo_mis.csv
Untracked: data/covar_corrected_myo-yes.vs.myo-no_4.batches_myo.csv
Untracked: data/covar_corrected_myo-yes.vs.myo-no_4.batches_myo_mis.csv
Untracked: data/covar_corrected_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo.csv
Untracked: data/covar_corrected_pbs-myo-yes.vs.pbs-myo-no_4.batches_myo_mis.csv
Untracked: data/e_4.batches_myo.RData
Untracked: data/e_snpg_samqc_4.batches_myo.RData
Untracked: data/errors_ind_4.batches_myo.RData
Untracked: data/genetic_map_4.batches_myo.csv
Untracked: data/genotype_errors_marker_4.batches_myo.RData
Untracked: data/genotype_freq_marker_4.batches_myo.RData
Untracked: data/gm_allqc_4.batches_myo.RData
Untracked: data/gm_allqc_4.batches_myo_mis.RData
Untracked: data/gm_samqc_4.batches_myo.RData
Untracked: data/gm_serreze.BC312.RData
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.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.ratiov_4.batches_myo.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.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_4.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_4.batches_myo_mis.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.4.batches_myo.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.4.batches_myo_mis.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.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.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.probs.freq.4.batches_myo.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.probs.freq.4.batches_myo_mis.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo.csv
Untracked: data/het-ici-myo-yes.vs.het-ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.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.csv
Untracked: data/het-ici.vs.het-pbs_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/het-ici.vs.het-pbs_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/het-ici.vs.het-pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo.csv
Untracked: data/het-ici.vs.het-pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
Untracked: data/het-ici.vs.het-pbs_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/het-ici.vs.het-pbs_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/het-ici.vs.het-pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
Untracked: data/het-ici.vs.het-pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.4.batches_myo.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.4.batches_myo_mis.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.probs.freq.4.batches_myo.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.probs.freq.4.batches_myo_mis.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.probs.freq.removed.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/het-ici.vs.het-pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.4.batches_myo.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.4.batches_myo_mis.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.probs.freq.4.batches_myo.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.probs.freq.4.batches_myo_mis.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/ici-myo-yes.vs.ici-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-10_peak.marker-UNC18805053_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-10_peak.marker-UNCHS029427_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-11_peak.marker-UNCHS031753_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-11_peak.marker-UNCHS031802_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-12_peak.marker-JAX00326005_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-12_peak.marker-UNC21995304_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-13_peak.marker-JAX00370189_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-13_peak.marker-UNCHS035661_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-14_peak.marker-UNC24597582_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-14_peak.marker-UNCHS039096_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-15_peak.marker-UNC25489755_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-15_peak.marker-UNCHS040614_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-16_peak.marker-UNCHS042686_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-17_peak.marker-UNCHS043777_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-17_peak.marker-UNCHS043880_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-18_peak.marker-UNC29296831_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-18_peak.marker-UNC29297751_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-19_peak.marker-UNC30069852_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-19_peak.marker-UNC30386742_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-1_peak.marker-UNCHS001121_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-1_peak.marker-UNCHS002308_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-2_peak.marker-UNC3990359_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-2_peak.marker-UNCHS006135_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-3_peak.marker-JAX00105915_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-3_peak.marker-UNC6020011_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-4_peak.marker-UNC8099452_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-4_peak.marker-UNC8161950_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-5_peak.marker-UNC9678100_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-5_peak.marker-UNC9678931_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-6_peak.marker-UNC12162881_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-6_peak.marker-backupUNC060363218_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-7_peak.marker-UNC12719038_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-7_peak.marker-UNCHS022024_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-8_peak.marker-UNC14948439_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-8_peak.marker-UNCHS023592_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-9_peak.marker-UNC16009822_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-9_peak.marker-UNC17271730_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_blup_sub_chr-X_peak.marker-UNC31358512_lod.drop-1.5_snpsqc_dis_no-x_updated_4.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_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-10_peak.marker-UNC18805053_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-10_peak.marker-UNCHS029427_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-11_peak.marker-UNCHS031753_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-11_peak.marker-UNCHS031802_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-12_peak.marker-JAX00326005_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-12_peak.marker-UNC21995304_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-13_peak.marker-JAX00370189_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-13_peak.marker-UNCHS035661_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-14_peak.marker-UNC24597582_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-14_peak.marker-UNCHS039096_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-15_peak.marker-UNC25489755_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-15_peak.marker-UNCHS040614_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-16_peak.marker-UNCHS042686_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-17_peak.marker-UNCHS043777_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-17_peak.marker-UNCHS043880_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-18_peak.marker-UNC29296831_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-18_peak.marker-UNC29297751_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-19_peak.marker-UNC30069852_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-19_peak.marker-UNC30386742_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-1_peak.marker-UNCHS001121_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-1_peak.marker-UNCHS002308_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-2_peak.marker-UNC3990359_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-2_peak.marker-UNCHS006135_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-3_peak.marker-JAX00105915_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-3_peak.marker-UNC6020011_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-4_peak.marker-UNC8099452_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-4_peak.marker-UNC8161950_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-5_peak.marker-UNC9678100_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-5_peak.marker-UNC9678931_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-6_peak.marker-UNC12162881_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-6_peak.marker-backupUNC060363218_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-7_peak.marker-UNC12719038_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-7_peak.marker-UNCHS022024_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-8_peak.marker-UNC14948439_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-8_peak.marker-UNCHS023592_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-9_peak.marker-UNC16009822_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-9_peak.marker-UNC17271730_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_genes_chr-X_peak.marker-UNC31358512_lod.drop-1.5_snpsqc_dis_no-x_updated_4.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_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_gm_qtl_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed.csv
Untracked: data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed.csv
Untracked: data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.probs.freq.4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.probs.freq.removed.csv
Untracked: data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.probs.freq.removed_4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/ici-sick.vs.ici-eoi_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv
Untracked: data/ici.vs.pbs_gm_qtl_snpsqc_dis_no-x_updated_4.batches_myo.csv
Untracked: data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo.csv
Untracked: data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
Untracked: data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
Untracked: data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.4.batches_myo.csv
Untracked: data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.4.batches_myo_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.4.batches_myo.csv
Untracked: data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo_mis.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.4.batches_myo.csv
Untracked: data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.4.batches_myo_mis.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.4.batches_myo.csv
Untracked: data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv
Untracked: data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
Untracked: data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo.csv
Untracked: data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
Untracked: data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
Untracked: data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.4.batches_myo.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.4.batches_myo_mis.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.probs.freq.4.batches_myo.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.probs.freq.4.batches_myo_mis.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.probs.freq.removed.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/myo-yes.vs.myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.4.batches_myo.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.4.batches_myo_mis.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.probs.freq.4.batches_myo.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.probs.freq.4.batches_myo_mis.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.probs.freq.removed.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.4.batches_myo_mis.csv
Untracked: data/pbs-myo-yes.vs.pbs-myo-no_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv
Untracked: data/percent_missing_id_4.batches_myo.RData
Untracked: data/percent_missing_marker_4.batches_myo.RData
Untracked: data/pheno_4.batches_myo.csv
Untracked: data/physical_map_4.batches_myo.csv
Untracked: data/qc_info_bad_sample_4.batches_myo.RData
Untracked: data/sample_geno_AHB_4.batches_myo.csv
Untracked: data/sample_geno_bc_4.batches_myo.csv
Untracked: data/serreze_probs_4.batches_myo.rds
Untracked: data/serreze_probs_allqc_4.batches_myo.rds
Untracked: data/serreze_probs_allqc_4.batches_myo_mis.rds
Untracked: data/summary.cg_4.batches_myo.RData
Untracked: output/Percent_missing_genotype_data_4.batches_myo.pdf
Untracked: output/Percent_missing_genotype_data_per_marker_4.batches_myo.pdf
Untracked: output/Proportion_matching_genotypes_before_removal_of_bad_samples_4.batches_myo.pdf
Untracked: output/genotype_error_marker_4.batches_myo.pdf
Untracked: output/genotype_frequency_marker_4.batches_myo.pdf
Unstaged changes:
Modified: analysis/index_5.batches.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.
| abbreviations for strains: | AB: het; AA: hom |
| type of cross: | Backcross |
| number of mice phenotyped: | 217 |
| total number of mice phenotypes: | 2 [1 binary/1 quantiative] |
| phenotypes: | myocarditis status/group [binary] & age of onset [continuous] |
| number of mice: | 217 |
| number of markers: | 137302 |
| covariates: | sex [F: 196; M: 21] ; and others depending on samples used in analysis |
Xcovar); using sex as a
covariater/qtl2 does not allow for the
inclusion of a kinship matrix in this type of modelICI vs EOIICI Sick vs ICI EOIICI vs PBSICI Myocarditis Yes vs ICI Myocarditis NoPBS Myocarditis Yes vs PBS Myocarditis NoMyocarditis Yes vs Myocarditis NoHetero: ICI vs PBSHetero: ICI Myocarditis Yes vs ICI Myocarditis NoThe following analysis has been done with age of onset
as all samples have a value:….
disease status was used as a binary covariate (that is,
diabetes/no diabetes or yes/no) for analyses in each sample setXcovar) 4 no kinship included….
ICI vs EOIICI Sick vs ICI EOIICI vs PBSICI Myocarditis Yes vs ICI Myocarditis NoPBS Myocarditis Yes vs PBS Myocarditis NoMyocarditis Yes vs Myocarditis NoHetero: ICI vs PBSHetero: ICI Myocarditis Yes vs ICI Myocarditis No….
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_1.41 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_0.6.30 utf8_1.2.2
[9] R6_2.5.1 cellranger_1.1.0 RSQLite_2.2.19 evaluate_0.18
[13] httr_1.4.4 pillar_1.8.1 rlang_1.0.6 rstudioapi_0.14
[17] blob_1.2.3 whisker_0.4.1 callr_3.7.3 jquerylib_0.1.4
[21] rmarkdown_2.18 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_0.35 pkgconfig_2.0.3 systemfonts_1.0.4 htmltools_0.5.3
[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_3.4.1 stringi_1.7.8 cachem_1.0.6
[49] fs_1.5.2 promises_1.2.0.1 getopt_1.20.3 xml2_1.3.3
[53] bslib_0.4.1 generics_0.1.3 vctrs_0.5.1 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_1.1.0 yaml_2.3.6 colorspace_2.0-3
[65] rvest_1.0.3 memoise_2.0.1 sass_0.4.4