Last updated: 2020-11-04

Checks: 2 0

Knit directory: csna_workflow/

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


Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

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 2f3a962. 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:    .Rhistory
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/figure/

Untracked files:
    Untracked:  analysis/.nfs0000000135a08b9b00002448
    Untracked:  analysis/.nfs0000000135a08ba50000244a
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a1.R
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a1.err
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a1.out
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a1.sh
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a2.R
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a2.err
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a2.out
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a2.sh
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a3.R
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a3.err
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a3.out
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a3.sh
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a4.R
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a4.err
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a4.out
    Untracked:  analysis/19_qtl_analysis_RTG20_GS_a4.sh
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a1.R
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a1.err
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a1.out
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a1.sh
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a2.R
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a2.err
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a2.out
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a2.sh
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a3.R
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a3.err
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a3.out
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a3.sh
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a4.R
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a4.err
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a4.out
    Untracked:  analysis/19_qtl_analysis_RTG20_G_a4.sh
    Untracked:  analysis/csna_image.sif
    Untracked:  analysis/scripts/
    Untracked:  analysis/temp/
    Untracked:  analysis/workflow_proc.R
    Untracked:  analysis/workflow_proc.sh
    Untracked:  analysis/workflow_proc.stderr
    Untracked:  analysis/workflow_proc.stdout
    Untracked:  code/reconst_utils.R
    Untracked:  data/69k_grid_pgmap.RData
    Untracked:  data/FinalReport/
    Untracked:  data/GCTA/
    Untracked:  data/GM/
    Untracked:  data/Jackson_Lab_11_batches/
    Untracked:  data/Jackson_Lab_12_batches/
    Untracked:  data/Jackson_Lab_Bubier_MURGIGV01/
    Untracked:  data/Jackson_Lab_Gagnon/
    Untracked:  data/RTG/
    Untracked:  data/cc_variants.sqlite
    Untracked:  data/marker_grid_0.02cM_plus.txt
    Untracked:  data/mouse_genes_mgi.sqlite
    Untracked:  data/pheno/
    Untracked:  output/AfterQC_Percent_missing_genotype_data.pdf
    Untracked:  output/AfterQC_Proportion_matching_genotypes_after_removal_of_bad_samples.pdf
    Untracked:  output/AfterQC_Proportion_matching_genotypes_before_removal_of_bad_samples.pdf
    Untracked:  output/AfterQC_number_crossover.pdf
    Untracked:  output/DO_Gigamuga_chr2_WSB_G21.png
    Untracked:  output/DO_Gigamuga_chr2_WSB_G22.png
    Untracked:  output/DO_Gigamuga_chr2_WSB_G23.png
    Untracked:  output/DO_Gigamuga_chr2_WSB_G25.png
    Untracked:  output/DO_Gigamuga_chr2_WSB_G29.png
    Untracked:  output/DO_Gigamuga_chr2_WSB_G30.png
    Untracked:  output/DO_Gigamuga_chr2_WSB_G31.png
    Untracked:  output/DO_Gigamuga_chr2_WSB_G32.png
    Untracked:  output/DO_Gigamuga_chr2_WSB_G33.png
    Untracked:  output/DO_Gigamuga_founder_proportions_G21.png
    Untracked:  output/DO_Gigamuga_founder_proportions_G22.png
    Untracked:  output/DO_Gigamuga_founder_proportions_G23.png
    Untracked:  output/DO_Gigamuga_founder_proportions_G25.png
    Untracked:  output/DO_Gigamuga_founder_proportions_G29.png
    Untracked:  output/DO_Gigamuga_founder_proportions_G30.png
    Untracked:  output/DO_Gigamuga_founder_proportions_G31.png
    Untracked:  output/DO_Gigamuga_founder_proportions_G32.png
    Untracked:  output/DO_Gigamuga_founder_proportions_G33.png
    Untracked:  output/DO_Gigamuga_founder_proportions_chr2_G21.png
    Untracked:  output/DO_Gigamuga_founder_proportions_chr2_G22.png
    Untracked:  output/DO_Gigamuga_founder_proportions_chr2_G23.png
    Untracked:  output/DO_Gigamuga_founder_proportions_chr2_G25.png
    Untracked:  output/DO_Gigamuga_founder_proportions_chr2_G29.png
    Untracked:  output/DO_Gigamuga_founder_proportions_chr2_G30.png
    Untracked:  output/DO_Gigamuga_founder_proportions_chr2_G31.png
    Untracked:  output/DO_Gigamuga_founder_proportions_chr2_G32.png
    Untracked:  output/DO_Gigamuga_founder_proportions_chr2_G33.png
    Untracked:  output/DO_recom_block_size_G21.png
    Untracked:  output/DO_recom_block_size_G22.png
    Untracked:  output/DO_recom_block_size_G23.png
    Untracked:  output/DO_recom_block_size_G25.png
    Untracked:  output/DO_recom_block_size_G29.png
    Untracked:  output/DO_recom_block_size_G30.png
    Untracked:  output/DO_recom_block_size_G31.png
    Untracked:  output/DO_recom_block_size_G32.png
    Untracked:  output/DO_recom_block_size_G33.png
    Untracked:  output/Histgram_Prj01_RL-Acquisition_preqc_02142020.pdf
    Untracked:  output/Histgram_Prj01_RL-Reversal_preqc_02142020.pdf
    Untracked:  output/Histgram_Prj02_Sensitization_preqc_02142020.pdf
    Untracked:  output/Histgram_Prj04_IVSA_preqc_02142020.pdf
    Untracked:  output/Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv
    Untracked:  output/Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv
    Untracked:  output/Novelty_residuals_RankNormal_datarelease_12182019-genelist.csv
    Untracked:  output/Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv
    Untracked:  output/Percent_genotype_errors_obs_vs_predicted.pdf
    Untracked:  output/Percent_missing_genotype_data.pdf
    Untracked:  output/Percent_missing_genotype_data_per_marker.pdf
    Untracked:  output/Proportion_matching_genotypes_after_removal_of_bad_samples.pdf
    Untracked:  output/Proportion_matching_genotypes_after_removal_samples_percent_missing_5.pdf
    Untracked:  output/Proportion_matching_genotypes_before_removal_of_bad_samples.pdf
    Untracked:  output/Proportion_matching_genotypes_before_removal_samples.pdf
    Untracked:  output/RTG/
    Untracked:  output/blup/
    Untracked:  output/condi.m2.Novelty_residuals_RankNormal_datarelease_12182019_genomescan.pdf
    Untracked:  output/condi.m2.qtl.blup_Novelty_residuals_RankNormal_datarelease_12182019_coeffgeneplot.pdf
    Untracked:  output/condi.m2.qtl.out.RData
    Untracked:  output/conditional.69k.Novelty_residuals_RankNormal_datarelease_12182019-genelist.csv
    Untracked:  output/conditional.69k.Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv
    Untracked:  output/conditional.Novelty_residuals_RankNormal_datarelease_12182019-genelist.csv
    Untracked:  output/conditional.Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv
    Untracked:  output/conditional.m2.69k.Novelty_residuals_RankNormal_datarelease_12182019.RData
    Untracked:  output/conditional.m2.69k.Novelty_residuals_RankNormal_datarelease_12182019_coeffgeneplot.pdf
    Untracked:  output/conditional.m2.69k.Novelty_residuals_RankNormal_datarelease_12182019_genomescan.pdf
    Untracked:  output/conditional.m2.Novelty_residuals_RankNormal_datarelease_12182019.RData
    Untracked:  output/conditional.m2.Novelty_residuals_RankNormal_datarelease_12182019_coeffgeneplot.pdf
    Untracked:  output/conditional.m2.Novelty_residuals_RankNormal_datarelease_12182019_genomescan.pdf
    Untracked:  output/conditional.m2.qtl.out.RData
    Untracked:  output/conditional_m2.Novelty_residuals_RankNormal_datarelease_07302918_genomescan.pdf
    Untracked:  output/conditional_m2.Novelty_residuals_RankNormal_datarelease_12182019_genomescan.pdf
    Untracked:  output/genotype_error_marker.pdf
    Untracked:  output/genotype_frequency_marker.pdf
    Untracked:  output/m1.Novelty_resids_datarelease_07302918.RData
    Untracked:  output/m1.Novelty_resids_datarelease_07302918_coeffgeneplot.pdf
    Untracked:  output/m1.Novelty_resids_datarelease_07302918_genomescan.pdf
    Untracked:  output/m1.Novelty_resids_datarelease_12182019.RData
    Untracked:  output/m1.Novelty_resids_datarelease_12182019_coeffgeneplot.pdf
    Untracked:  output/m1.Novelty_resids_datarelease_12182019_genomescan.pdf
    Untracked:  output/m1.Novelty_residuals_RankNormal_datarelease_07302918.RData
    Untracked:  output/m1.Novelty_residuals_RankNormal_datarelease_07302918_genomescan.pdf
    Untracked:  output/m1.Novelty_residuals_RankNormal_datarelease_12182019.RData
    Untracked:  output/m1.Novelty_residuals_RankNormal_datarelease_12182019_coeffgeneplot.pdf
    Untracked:  output/m1.Novelty_residuals_RankNormal_datarelease_12182019_genomescan.pdf
    Untracked:  output/m2.69k.Novelty_residuals_RankNormal_datarelease_12182019.RData
    Untracked:  output/m2.69k.Novelty_residuals_RankNormal_datarelease_12182019_coeffgeneplot.pdf
    Untracked:  output/m2.69k.Novelty_residuals_RankNormal_datarelease_12182019_genomescan.pdf
    Untracked:  output/m2.69k.Prj01_RL-Acquisition_preqc_02142020.RData
    Untracked:  output/m2.69k.Prj01_RL-Reversal_preqc_02142020.RData
    Untracked:  output/m2.69k.Prj02_Sensitization_preqc_02142020.RData
    Untracked:  output/m2.69k.Prj04_IVSA_preqc_02142020.RData
    Untracked:  output/m2.Novelty_resids_datarelease_07302918.RData
    Untracked:  output/m2.Novelty_resids_datarelease_07302918_genomescan.pdf
    Untracked:  output/m2.Novelty_resids_datarelease_12182019.RData
    Untracked:  output/m2.Novelty_resids_datarelease_12182019_coeffgeneplot.pdf
    Untracked:  output/m2.Novelty_resids_datarelease_12182019_genomescan.pdf
    Untracked:  output/m2.Novelty_residuals_RankNormal_datarelease_07302918.RData
    Untracked:  output/m2.Novelty_residuals_RankNormal_datarelease_07302918_genomescan.pdf
    Untracked:  output/m2.Novelty_residuals_RankNormal_datarelease_12182019.RData
    Untracked:  output/m2.Novelty_residuals_RankNormal_datarelease_12182019_coeffgeneplot.pdf
    Untracked:  output/m2.Novelty_residuals_RankNormal_datarelease_12182019_genomescan.pdf
    Untracked:  output/m2.Prj01_RL-Acquisition_preqc_02142020.RData
    Untracked:  output/m2.Prj01_RL-Acquisition_preqc_02142020_qtl2scan.pdf
    Untracked:  output/m2.Prj01_RL-Reversal_preqc_02142020.RData
    Untracked:  output/m2.Prj01_RL-Reversal_preqc_02142020_qtl2scan.pdf
    Untracked:  output/m2.Prj02_Sensitization_preqc_02142020.RData
    Untracked:  output/m2.Prj02_Sensitization_preqc_02142020_qtl2scan.pdf
    Untracked:  output/m2.Prj04_IVSA_preqc_02142020.RData
    Untracked:  output/m2.Prj04_IVSA_preqc_02142020_qtl2scan.pdf
    Untracked:  output/m3.Novelty_resids_datarelease_07302918.RData
    Untracked:  output/m3.Novelty_resids_datarelease_07302918_genomescan.pdf
    Untracked:  output/m3.Novelty_resids_datarelease_12182019.RData
    Untracked:  output/m3.Novelty_resids_datarelease_12182019_coeffgeneplot.pdf
    Untracked:  output/m3.Novelty_resids_datarelease_12182019_genomescan.pdf
    Untracked:  output/m3.Novelty_residuals_RankNormal_datarelease_07302918.RData
    Untracked:  output/m3.Novelty_residuals_RankNormal_datarelease_07302918_genomescan.pdf
    Untracked:  output/m3.Novelty_residuals_RankNormal_datarelease_12182019.RData
    Untracked:  output/m3.Novelty_residuals_RankNormal_datarelease_12182019_coeffgeneplot.pdf
    Untracked:  output/m3.Novelty_residuals_RankNormal_datarelease_12182019_genomescan.pdf
    Untracked:  output/num.geno.pheno.in.Novelty_resids_datarelease_07302918.csv
    Untracked:  output/num.geno.pheno.in.Novelty_resids_datarelease_12182019.csv
    Untracked:  output/num.geno.pheno.in.Novelty_residuals_RankNormal_datarelease_07302918.csv
    Untracked:  output/num.geno.pheno.in.Novelty_residuals_RankNormal_datarelease_12182019.csv
    Untracked:  output/number_crossover.pdf
    Untracked:  output/permu/
    Untracked:  output/prop_across_generation_chr_p.RData

Unstaged changes:
    Modified:   README.md
    Modified:   _workflowr.yml
    Deleted:    analysis/01_geneseek2qtl2.R
    Deleted:    analysis/02_geneseek2intensity.R
    Deleted:    analysis/03_firstgm2genoprobs.R
    Deleted:    analysis/04_diagnosis_qc_gigamuga_11_batches.Rmd
    Deleted:    analysis/04_diagnosis_qc_gigamuga_nine_batches.R
    Deleted:    analysis/04_diagnosis_qc_gigamuga_nine_batches.Rmd
    Deleted:    analysis/05_after_diagnosis_qc_gigamuga_11_batches.Rmd
    Deleted:    analysis/05_after_diagnosis_qc_gigamuga_nine_batches.R
    Deleted:    analysis/05_after_diagnosis_qc_gigamuga_nine_batches.Rmd
    Deleted:    analysis/06_final_pr_apr_69K.R
    Deleted:    analysis/07.1_html_founder_prop.R
    Deleted:    analysis/07_recomb_size_founder_prop.R
    Deleted:    analysis/07_recomb_size_founder_prop.Rmd
    Deleted:    analysis/08_gcta_herit.R
    Deleted:    analysis/09_qtlmapping.R
    Deleted:    analysis/10_qtl_permu.R
    Deleted:    analysis/11_qtl_blup.R
    Deleted:    analysis/12_plot_69k_qtl_mapping_2.Rmd
    Deleted:    analysis/12_plot_qtl_mapping_1.Rmd
    Deleted:    analysis/12_plot_qtl_mapping_2.Rmd
    Deleted:    analysis/13_plot_69k_conditional_m2_qtlmapping.Rmd
    Deleted:    analysis/13_plot_conditional_m2_qtlmapping.Rmd
    Deleted:    analysis/16_diagnosis_qc_gigamuga_gagnon.Rmd
    Deleted:    analysis/16_diagnosis_qc_gigamuga_gagnon2.Rmd
    Deleted:    analysis/17_plot_qtl_mapping.Rmd
    Deleted:    analysis/run_01_geneseek2qtl2.R
    Deleted:    analysis/run_02_geneseek2intensity.R
    Deleted:    analysis/run_03_firstgm2genoprobs.R
    Deleted:    analysis/run_04_diagnosis_qc_gigamuga_nine_batches.R
    Deleted:    analysis/run_05_after_diagnosis_qc_gigamuga_nine_batches.R
    Deleted:    analysis/run_06_final_pr_apr_69K.R
    Deleted:    analysis/run_07.1_html_founder_prop.R
    Deleted:    analysis/run_07_recomb_size_founder_prop.R
    Deleted:    analysis/run_08_gcta_herit.R
    Deleted:    analysis/run_09_qtlmapping.R
    Deleted:    analysis/run_10_qtl_permu.R
    Deleted:    analysis/run_11_qtl_blup.R

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.


These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.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
Rmd 2f3a962 xhyuo 2020-11-04 12_batches
html 4794cfe xhyuo 2020-10-21 Build site.
Rmd f290bff xhyuo 2020-10-21 new
html d8fe998 xhyuo 2020-10-19 Build site.
html 27b48ff xhyuo 2020-02-25 Build site.
html 0404d44 xhyuo 2020-02-25 Build site.
Rmd 259f3a5 xhyuo 2020-02-25 12_plot_69k_qtl_mapping_2.Rmd
html 4aeac6f xhyuo 2020-02-25 Build site.
html a8606a2 xhyuo 2020-02-25 Build site.
html 693e807 xhyuo 2020-02-19 Build site.
html 00d2604 xhyuo 2020-02-19 Build site.
html 0632c4a xhyuo 2020-02-18 Build site.
html a0daa3a xhyuo 2020-02-18 Build site.
html 481cb4d xhyuo 2020-02-17 Build site.
html c4f4559 xhyuo 2020-02-17 Build site.
html d977cdc xhyuo 2020-02-16 Build site.
html 6861ae7 xhyuo 2020-02-16 Build site.
html a2f202a xhyuo 2020-01-09 Build site.
html 1b2c849 xhyuo 2020-01-09 Build site.
html c5ca735 xhyuo 2020-01-07 Build site.
html 626668d xhyuo 2020-01-07 Build site.
html 8d8f9b4 xhyuo 2019-12-27 Build site.
html 2c6b563 xhyuo 2019-12-03 Build site.
html 81802a2 xhyuo 2019-12-02 Build site.
Rmd 63c6284 xhyuo 2019-12-02 04_diagnosis_qc_gigamuga_11_batches.Rmd
html a7547b3 xhyuo 2019-12-01 Build site.
Rmd 2e2a837 xhyuo 2019-12-01 04_diagnosis_qc_gigamuga_11_batches.Rmd
html efed06b xhyuo 2019-10-21 Build site.
html f187b99 xhyuo 2019-10-21 Build site.
html d25bab6 xhyuo 2019-10-21 Build site.
Rmd 45cb7a7 xhyuo 2019-10-21 13_plot_conditional_m2_qtlmapping.Rmd
html 58d4c4e xhyuo 2019-10-20 Build site.
html 51b872f xhyuo 2019-10-20 Build site.
Rmd 6c3b9fc xhyuo 2019-10-20 wflow_publish(files = file)
html a6d6886 xhyuo 2019-10-20 Build site.
html e899cf1 xhyuo 2019-10-04 Build site.
html 7b693e9 xhyuo 2019-10-02 Build site.
html 463afa3 xhyuo 2019-10-02 Build site.
html a28dfe6 xhyuo 2019-10-02 Build site.
html e79d270 xhyuo 2019-10-02 Build site.
html 13d7e29 xhyuo 2019-10-02 Build site.
Rmd af8eb36 xhyuo 2019-10-02 12_plot_qtl_mapping_1.Rmd
html c3ee11a xhyuo 2019-09-23 Build site.
html 97188bc xhyuo 2019-09-23 Build site.
html 0d00279 xhyuo 2019-09-23 Build site.
html 27c1d86 xhyuo 2019-09-23 Build site.
html e271330 xhyuo 2019-09-22 Build site.
html 1e4e3f7 xhyuo 2019-09-22 Build site.
Rmd ed97ced xhyuo 2019-09-22 wflow_publish(c(“analysis/index.Rmd”, “analysis/about.Rmd”,
Rmd 898ff80 xhyuo 2019-09-22 Start workflowr project.

1 Data transformation from Finalreport.txt to qtl2 for 12 batches

2 Grab intensities from GeneSeek FinalReport.txt files convert them to a single big data frame

3 First time to calculate genoprobs, maxmarg, crossover, errorlod, snpg for the qc diagnositics

4 Genotype diagnostics for diversity outbred mice of 12 batches

5 After QC, genotype diagnostics

6 Calculation of the genoprobs after qc and do interpolatino to 69K grid

7 Plot the recombination block size and founder props across all generations

8 GCTA heritability

9 qtl mapping

10 qtl permutation

11 qtl blup

12 plot qtl mapping

13 conditional_m2_qtlmapping

14 geneseek2qtl2fst_Gagnon

15 firstgm2genoprobs_Gagnon

16 diagnosis_qc_gigamuga_gagnon