plot scan result for conditional_m2.Novelty_residuals_RankNormal_datarelease_12182019

Last updated: 2020-02-25

Checks: 7 0

Knit directory: csna_workflow/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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.

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(20190918)

The command set.seed(20190918) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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

Cache: none

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

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 2fa487b

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

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:    analysis/.Rhistory

Untracked files:
    Untracked:  analysis/.nfs0000000135a08b9b00002448
    Untracked:  analysis/.nfs0000000135a08ba50000244a
    Untracked:  analysis/.nfs0000000159105b68000007b2
    Untracked:  analysis/01_geneseek2qtl2.script
    Untracked:  analysis/02_geneseek2intensity.script
    Untracked:  analysis/03_2_firstgm2genoprobs.R
    Untracked:  analysis/03_2_firstgm2genoprobs.script
    Untracked:  analysis/03_firstgm2genoprobs.script
    Untracked:  analysis/04_diagnosis_qc_gigamuga_11_batches.R
    Untracked:  analysis/04_diagnosis_qc_gigamuga_11_batches.script
    Untracked:  analysis/04_diagnosis_qc_gigamuga_nine_batches.script
    Untracked:  analysis/05_after_diagnosis_qc_gigamuga_11_batches.R
    Untracked:  analysis/05_after_diagnosis_qc_gigamuga_11_batches.script
    Untracked:  analysis/05_after_diagnosis_qc_gigamuga_nine_batches.script
    Untracked:  analysis/06_final_pr_apr_69K.script
    Untracked:  analysis/07.1_html_founder_prop.script
    Untracked:  analysis/07_recomb_size_founder_prop.script
    Untracked:  analysis/08.0_11_batches_gcta.sh
    Untracked:  analysis/08.1_11_batches_merge_plink.sh
    Untracked:  analysis/08.1_11_batches_merge_plink.sh.e11230968
    Untracked:  analysis/08.1_11_batches_merge_plink.sh.o11230968
    Untracked:  analysis/08_gcta_herit_2.R
    Untracked:  analysis/09_69k_qtlmapping.R
    Untracked:  analysis/10_69k_qtl_permu.R
    Untracked:  analysis/11_69k_qtl_blup.R
    Untracked:  analysis/12_plot_69k_qtl_mapping.R
    Untracked:  analysis/12_plot_69k_qtl_mapping.script
    Untracked:  analysis/12_plot_qtl_mapping.R
    Untracked:  analysis/12_plot_qtl_mapping.script
    Untracked:  analysis/13_all_plot.R
    Untracked:  analysis/13_all_plot.script
    Untracked:  analysis/13_conditional_69k_blup.R
    Untracked:  analysis/13_conditional_69k_qtlmapping.R
    Untracked:  analysis/13_conditional_blup.R
    Untracked:  analysis/13_conditional_m2_qtlmapping.R
    Untracked:  analysis/13_conditional_m2_qtlmapping.script
    Untracked:  analysis/13_conditional_qtlmapping.R
    Untracked:  analysis/13_plot_69k_conditional_m2_qtlmapping.R
    Untracked:  analysis/13_plot_69k_conditional_m2_qtlmapping.script
    Untracked:  analysis/13_plot_conditional_m2_qtlmapping.R
    Untracked:  analysis/13_plot_conditional_m2_qtlmapping.script
    Untracked:  analysis/14_geneseek2qtl2fst_Gagnon.R
    Untracked:  analysis/14_geneseek2qtl2fst_Gagnon.script
    Untracked:  analysis/15_firstgm2genoprobs_Gagnon.R
    Untracked:  analysis/15_firstgm2genoprobs_Gagnon.script
    Untracked:  analysis/16_diagnosis_qc_gigamuga_gagnon.R
    Untracked:  analysis/16_diagnosis_qc_gigamuga_gagnon.script
    Untracked:  analysis/17_plot_qtl_mapping.R
    Untracked:  analysis/17_plot_qtl_mapping.script
    Untracked:  analysis/17_qtlmapping.R
    Untracked:  analysis/Novelty_no_outliers_datarelease_12182019.gcta.script
    Untracked:  analysis/Novelty_raw_datarelease_12182019.gcta.script
    Untracked:  analysis/Novelty_resids_datarelease_12182019.gcta.script
    Untracked:  analysis/Novelty_resids_datarelease_12182019_m1.script
    Untracked:  analysis/Novelty_resids_datarelease_12182019_m2.script
    Untracked:  analysis/Novelty_resids_datarelease_12182019_m3.script
    Untracked:  analysis/Novelty_residuals_RankNormal_datarelease_12182019.gcta.script
    Untracked:  analysis/Novelty_residuals_RankNormal_datarelease_12182019_69k_m2.script
    Untracked:  analysis/Novelty_residuals_RankNormal_datarelease_12182019_m1.script
    Untracked:  analysis/Novelty_residuals_RankNormal_datarelease_12182019_m2.script
    Untracked:  analysis/Novelty_residuals_RankNormal_datarelease_12182019_m3.script
    Untracked:  analysis/Prj01_RL-Acquisition_preqc_02142020.gcta.script
    Untracked:  analysis/Prj01_RL-Acquisition_preqc_02142020_m2.script
    Untracked:  analysis/Prj01_RL-Reversal_preqc_02142020.gcta.script
    Untracked:  analysis/Prj01_RL-Reversal_preqc_02142020_m2.script
    Untracked:  analysis/Prj02_Sensitization_preqc_02142020.gcta.script
    Untracked:  analysis/Prj02_Sensitization_preqc_02142020_m2.script
    Untracked:  analysis/Prj04_IVSA_preqc_02142020.gcta.script
    Untracked:  analysis/Prj04_IVSA_preqc_02142020_m2.script
    Untracked:  analysis/blup_14_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_14_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_14_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_14_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_14_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_14_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_15_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_15_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_15_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_15_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_15_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_15_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_16_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_16_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_16_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_16_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_16_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_16_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_17_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_17_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_17_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_17_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_17_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_17_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_18_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_18_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_18_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_18_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_18_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_18_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_19_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_19_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_19_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_19_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_19_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_19_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_20_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_20_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_20_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_20_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_20_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_20_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_21_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_21_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_21_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_21_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_21_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_21_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_22_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_22_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_22_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_22_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_22_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_22_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_23_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_23_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_23_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_23_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_23_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_23_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_24_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_24_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_24_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_24_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_24_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_24_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_25_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_25_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_25_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_25_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_25_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_25_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_26_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_26_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_26_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_26_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_26_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_26_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_27_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_27_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_27_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_27_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_27_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_27_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_28_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_28_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_28_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_28_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_28_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_28_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_29_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_29_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_29_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_29_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_29_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_29_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_30_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_30_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_30_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_30_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_30_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_30_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_31_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_31_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_31_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_31_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_31_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_31_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_32_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_32_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_32_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_32_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_32_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_32_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_33_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_33_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_33_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_33_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_33_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_33_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_34_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_34_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_34_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_34_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_34_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_34_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_35_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_35_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_35_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_35_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_35_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_35_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_36_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_36_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_36_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_36_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_36_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_36_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_37_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_37_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_37_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_37_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_37_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_37_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_38_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_38_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_38_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_38_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_38_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_38_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_39_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_39_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_39_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_39_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_39_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_39_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_40_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_40_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_40_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_40_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_40_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_40_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_41_m1_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_41_m1_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_41_m2_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_41_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_41_m3_Novelty_resids_datarelease_12182019.script
    Untracked:  analysis/blup_41_m3_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_14_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_15_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_16_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_17_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_18_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_19_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_20_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_21_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_22_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_23_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_24_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_25_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_26_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_27_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_28_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_29_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_30_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_31_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_32_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_33_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_34_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_35_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_36_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_37_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_38_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_39_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_40_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/blup_69k_41_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_Novelty_residuals_RankNormal_datarelease_12182019_m2.script
    Untracked:  analysis/conditional_69k_blup_14_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_15_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_16_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_17_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_18_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_19_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_20_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_21_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_22_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_23_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_24_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_25_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_26_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_27_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_28_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_29_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_30_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_31_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_32_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_33_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_34_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_35_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_36_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_37_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_38_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_39_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_40_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_69k_blup_41_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_Novelty_residuals_RankNormal_datarelease_12182019_m2.script
    Untracked:  analysis/conditional_blup_14_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_15_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_16_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_17_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_18_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_19_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_20_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_21_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_22_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_23_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_24_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_25_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_26_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_27_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_28_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_29_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_30_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_31_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_32_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_33_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_34_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_35_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_36_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_37_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_38_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_39_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_40_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/conditional_blup_41_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_10_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_11_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_12_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_13_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_14_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_15_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_16_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_17_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_18_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_19_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_1_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_20_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_21_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_22_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_23_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_24_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_25_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_26_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_27_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_28_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_29_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_2_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_30_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_31_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_32_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_33_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_34_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_35_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_36_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_37_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_38_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_39_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_3_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_40_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_41_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_42_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_43_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_44_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_45_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_46_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_47_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_48_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_49_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_4_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_50_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_5_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_10_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_11_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_12_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_13_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_14_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_15_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_16_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_17_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_18_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_19_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_1_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_20_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_21_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_22_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_23_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_24_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_25_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_26_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_27_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_28_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_29_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_2_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_30_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_31_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_32_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_33_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_34_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_35_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_36_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_37_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_38_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_39_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_3_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_40_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_41_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_42_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_43_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_44_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_45_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_46_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_47_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_48_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_49_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_4_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_50_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_5_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_6_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_7_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_8_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_69k_9_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_6_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_7_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_8_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/permu_9_m2_Novelty_residuals_RankNormal_datarelease_12182019.script
    Untracked:  analysis/run_04_diagnosis_qc_gigamuga_11_batches.R
    Untracked:  analysis/run_05_after_diagnosis_qc_gigamuga_11_batches.R
    Untracked:  analysis/run_09_69k_qtlmapping.R
    Untracked:  analysis/run_10_69k_qtl_permu.R
    Untracked:  analysis/run_10_69k_qtl_permu.e11543283
    Untracked:  analysis/run_10_69k_qtl_permu.e11548985
    Untracked:  analysis/run_10_69k_qtl_permu.o11543283
    Untracked:  analysis/run_10_69k_qtl_permu.o11548985
    Untracked:  analysis/run_10_qtl_permu.o11472940
    Untracked:  analysis/run_11_69k_qtl_blup.R
    Untracked:  analysis/run_11_69k_qtl_blup.e11543288
    Untracked:  analysis/run_11_69k_qtl_blup.e11560161
    Untracked:  analysis/run_11_69k_qtl_blup.o11543288
    Untracked:  analysis/run_11_69k_qtl_blup.o11560161
    Untracked:  analysis/run_12_plot_qtl_mapping.R
    Untracked:  analysis/run_13_conditional_69k_blup.R
    Untracked:  analysis/run_13_conditional_69k_qtlmapping.R
    Untracked:  analysis/run_13_conditional_69k_qtlmapping.R.e11560365
    Untracked:  analysis/run_13_conditional_69k_qtlmapping.R.o11560365
    Untracked:  analysis/run_13_conditional_blup.R
    Untracked:  analysis/run_13_conditional_qtlmapping.R
    Untracked:  analysis/run_13_conditional_qtlmapping.R.e11509917
    Untracked:  analysis/run_13_conditional_qtlmapping.R.o11509917
    Untracked:  analysis/run_13_plot_conditional_m2_qtlmapping.R
    Untracked:  analysis/run_14_geneseek2qtl2fst_Gagnon.R
    Untracked:  analysis/run_15_firstgm2genoprobs_Gagnon.R
    Untracked:  analysis/run_16_diagnosis_qc_gigamuga_gagnon.R
    Untracked:  analysis/run_17_gcta_herit.R
    Untracked:  analysis/run_17_qtlmapping.R
    Untracked:  analysis/run_run_09_qtlmapping.script
    Untracked:  analysis/run_run_10_69k_qtl_permu.script
    Untracked:  analysis/run_run_10_qtl_permu.script
    Untracked:  analysis/run_run_11_69k_qtl_blup.script
    Untracked:  analysis/run_run_11_qtl_blup.script
    Untracked:  analysis/run_run_13_conditional_69k_blup.script
    Untracked:  analysis/run_run_13_conditional_blup.script
    Untracked:  analysis/scriptout/
    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_Bubier_MURGIGV01/
    Untracked:  data/Jackson_Lab_Gagnon/
    Untracked:  data/cc_variants.sqlite
    Untracked:  data/marker_grid_0.02cM_plus.txt
    Untracked:  data/mouse_genes_mgi.sqlite
    Untracked:  data/pheno/
    Untracked:  docs/figure/13_plot_69k_conditional_m2_qtlmapping.Rmd/
    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/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_before_removal_of_bad_samples.pdf
    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.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.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
    Modified:   analysis/01_geneseek2qtl2.R
    Modified:   analysis/02_geneseek2intensity.R
    Modified:   analysis/03_firstgm2genoprobs.R
    Modified:   analysis/04_diagnosis_qc_gigamuga_nine_batches.R
    Modified:   analysis/06_final_pr_apr_69K.R
    Modified:   analysis/07.1_html_founder_prop.R
    Modified:   analysis/07_recomb_size_founder_prop.R
    Modified:   analysis/08_gcta_herit.R
    Modified:   analysis/09_qtlmapping.R
    Modified:   analysis/10_qtl_permu.R
    Modified:   analysis/11_qtl_blup.R
    Modified:   analysis/run_01_geneseek2qtl2.R
    Modified:   analysis/run_02_geneseek2intensity.R
    Modified:   analysis/run_03_firstgm2genoprobs.R
    Modified:   analysis/run_04_diagnosis_qc_gigamuga_nine_batches.R
    Modified:   analysis/run_05_after_diagnosis_qc_gigamuga_nine_batches.R
    Modified:   analysis/run_06_final_pr_apr_69K.R
    Modified:   analysis/run_07.1_html_founder_prop.R
    Modified:   analysis/run_07_recomb_size_founder_prop.R
    Modified:   analysis/run_08_gcta_herit.R
    Modified:   analysis/run_09_qtlmapping.R
    Modified:   analysis/run_10_qtl_permu.R
    Modified:   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 R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File	Version	Author	Date	Message
Rmd	2fa487b	xhyuo	2020-02-25	four_plots_Rmd
html	4aeac6f	xhyuo	2020-02-25	Build site.
Rmd	eb8fe4a	xhyuo	2020-02-25	13_plot_conditional_m2_qtlmapping.Rmd
html	d977cdc	xhyuo	2020-02-16	Build site.
html	a2f202a	xhyuo	2020-01-09	Build site.
Rmd	756b79a	xhyuo	2020-01-09	13_plot_conditional_m2_qtlmapping.Rmd
html	1b2c849	xhyuo	2020-01-09	Build site.
Rmd	0294e57	xhyuo	2020-01-09	13_plot_conditional_m2_qtlmapping.Rmd
html	626668d	xhyuo	2020-01-07	Build site.
html	8d8f9b4	xhyuo	2019-12-27	Build site.
Rmd	ae79216	xhyuo	2019-12-27	13_plot_conditional_m2_qtlmapping.Rmd
html	efed06b	xhyuo	2019-10-21	Build site.
Rmd	4472c2a	xhyuo	2019-10-21	13_plot_conditional_m2_qtlmapping.Rmd
html	f187b99	xhyuo	2019-10-21	Build site.
Rmd	613db85	xhyuo	2019-10-21	13_plot_conditional_m2_qtlmapping.Rmd
html	d25bab6	xhyuo	2019-10-21	Build site.
Rmd	45cb7a7	xhyuo	2019-10-21	13_plot_conditional_m2_qtlmapping.Rmd

plot scan result for conditional_m2.Novelty_residuals_RankNormal_datarelease_12182019

#   This script performs plotting on qtl conditional mapping for DO mice m2, Novelty_residuals_RankNormal_datarelease_12182019
library(qtl2)
library(ggplot2)
load("data/Jackson_Lab_11_batches/gm_DO2816_qc.RData")
pheno <- read.csv("data/pheno/Novelty_residuals_RankNormal_datarelease_12182019.csv", header = TRUE)

print("m2")

[1] "m2"

load("output/conditional.m2.Novelty_residuals_RankNormal_datarelease_12182019.RData")

#permutation results
#The default is to return the 5% significance thresholds. Thresholds for other (or for multiple) significance levels can be obtained via the alpha argument.
operm <- list()
for(i in c(1:50)){
  operm[[i]] <- get(load(paste0("output/permu/m2_Novelty_residuals_RankNormal_datarelease_12182019_", colnames(pheno)[14], "_", i, ".RData")))
  operm[[i]] <- operm[[i]]$OFA.total.distance.traveled
}
operm <- matrix(do.call(rbind, operm[c(1:50)]),ncol = 1)
class(operm) <- c("scan1perm", "matrix")
cutoff <- summary(operm, c(0.05, 0.1))[,1]

#genome-wide results
pdf(file = paste0("output/conditional.m2.Novelty_residuals_RankNormal_datarelease_12182019", "_genomescan.pdf"), width = 14)
for(i in names(condi.m2.qtl.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(condi.m2.qtl.out[[i]])*1.2 # overall maximum LOD score
  ymax <- ifelse(ymx > cutoff[1]*1.2, ymx, cutoff[1]*1.2)
  plot(condi.m2.qtl.out[[i]], gm_DO2816_qc$gmap, lodcolumn=1,
       col="slateblue", ylim=c(0, ymax),
       main=i)
  abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
  abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}
dev.off()

png 
  2

#load blup results
x <- list()
#colnames(pheno)[14:41]
for(i in colnames(pheno)[14:41]){
  y <- get(load(paste0("output/blup/conditional.m2.blup_Novelty_residuals_RankNormal_datarelease_12182019_",i,".RData")))
  x[[i]] <- y[[i]]
}
condi.m2.qtl.blup = x

#coeffects plot
condi.m2.qtl.peak <- list()
pdf(file = paste0("output/conditional.m2.Novelty_residuals_RankNormal_datarelease_12182019", "_coeffgeneplot.pdf"), width = 14)
#names(condi.m2.qtl.out)
for(i in names(condi.m2.qtl.out)){
  #peak
  condi.m2.qtl.peak[[i]] <- find_peaks(condi.m2.qtl.out[[i]], gm_DO2816_qc$gmap,
                                       threshold=maxlod(condi.m2.qtl.out[[i]])-0.001,
                                       drop = 1.5)
  condi.m2.qtl.peak[[i]]$lodcolumn <- i
  print(condi.m2.qtl.peak[[i]])
  
  chr <- as.character(condi.m2.qtl.peak[[i]][condi.m2.qtl.peak[[i]]$lodcolumn == i,"chr"])
  par(mar=c(4.1, 4.1, 1.6, 1.6))
#  plot_coefCC(condi.m2.coef[[i]],
#               gm_DO2816_qc$gmap[chr],
#               scan1_output=condi.m2.qtl.out[[i]],
#               bgcolor="gray95", #legend="bottomleft",
#               main =i)
  plot_coefCC(condi.m2.qtl.blup[[i]],
              gm_DO2816_qc$gmap[chr],
              scan1_output=condi.m2.qtl.out[[i]],
              bgcolor="gray95", #legend="bottomleft",
              main =i)
#   plot(condi.m2.snps[[i]]$lod,
#         condi.m2.snps[[i]]$snpinfo,
#         drop_hilit=1.5,
#         genes=condi.m2.genes[[i]],
#         main = i)
}

  lodindex                   lodcolumn chr    pos      lod ci_lo  ci_hi
1        1 OFA.total.distance.traveled  10 76.513 8.446601 73.92 77.149

  lodindex                   lodcolumn chr    pos     lod  ci_lo  ci_hi
1        1 OFA.distance.traveled.slope  18 16.723 7.81814 16.071 23.093

  lodindex                lodcolumn chr   pos      lod  ci_lo  ci_hi
1        1 OFA.total.time.in.corner   2 49.76 8.521552 49.072 50.588

  lodindex                   lodcolumn chr    pos      lod ci_lo  ci_hi
1        1 OFA.total.time.in.perimeter  10 74.106 9.784588 73.92 74.503

  lodindex                lodcolumn chr    pos      lod  ci_lo  ci_hi
1        1 OFA.total.time.in.center   6 46.518 8.016775 46.052 46.975

  lodindex                 lodcolumn chr    pos      lod ci_lo  ci_hi
1        1 OFA.total.ambulatory.time  10 73.985 8.645845 73.92 76.531

  lodindex                                lodcolumn chr    pos     lod
1        1 OFA.total.distance.traveled.in.perimeter  10 74.074 10.7076
  ci_lo  ci_hi
1 73.92 77.088

  lodindex                             lodcolumn chr    pos      lod ci_lo
1        1 OFA.total.distance.traveled.in.center   6 46.616 7.217382 2.535
   ci_hi
1 47.044

  lodindex                             lodcolumn chr    pos      lod
1        1 OFA.total.distance.traveled.in.corner  16 16.709 8.297126
   ci_lo  ci_hi
1 16.266 16.814

  lodindex           lodcolumn chr   pos      lod ci_lo  ci_hi
1        1 OFA.pct.dist.center   6 5.541 7.769937 3.226 51.574

  lodindex           lodcolumn chr    pos      lod  ci_lo  ci_hi
1        1 OFA.pct.dist.corner   6 51.573 7.688641 45.925 52.554

  lodindex              lodcolumn chr    pos      lod  ci_lo  ci_hi
1        1 OFA.pct.dist.perimeter   1 32.928 9.274424 31.684 33.569

  lodindex           lodcolumn chr    pos      lod  ci_lo  ci_hi
1        1 OFA.pct.time.center   1 33.365 8.028654 31.193 33.554

  lodindex           lodcolumn chr   pos      lod ci_lo  ci_hi
1        1 OFA.pct.time.corner   6 8.797 6.995772 5.276 46.975

  lodindex              lodcolumn chr    pos      lod  ci_lo  ci_hi
1        1 OFA.pct.time.perimeter   1 32.929 8.290732 31.582 33.554

  lodindex                        lodcolumn chr    pos      lod ci_lo
1        1 OFA.distance.traveled.first.five  10 73.985 11.43961 73.92
   ci_hi
1 74.248

  lodindex                       lodcolumn chr    pos      lod ci_lo ci_hi
1        1 OFA.distance.traveled.last.five   5 10.663 8.135841 10.51 11.96

  lodindex                         lodcolumn chr    pos      lod  ci_lo
1        1 LD.pct.distance.traveled.in.light  15 34.548 7.257033 33.831
   ci_hi
1 34.552

  lodindex                       lodcolumn chr    pos      lod ci_lo
1        1 LD.pct.ambulatory.time.in.light   8 23.078 6.753169 19.37
   ci_hi
1 24.497

  lodindex                    lodcolumn chr   pos      lod ci_lo ci_hi
1        1 LD.pct.resting.time.in.light  10 6.973 6.706699 5.865 7.626

  lodindex            lodcolumn chr    pos      lod  ci_lo  ci_hi
1        1 LD.pct.time.in.light  15 34.078 6.881954 32.361 34.552

  lodindex                         lodcolumn chr    pos      lod ci_lo
1        1 LD.pct.ambulatory.Counts.in.light   8 23.078 7.111158 19.37
   ci_hi
1 23.517

  lodindex            lodcolumn chr   pos      lod ci_lo ci_hi
1        1 LD.total.transitions   6 2.158 7.096609 1.923 2.253

  lodindex        lodcolumn chr    pos      lod ci_lo  ci_hi
1        1 HB.Total.Entries   2 48.993 7.758587 19.57 49.042

  lodindex        lodcolumn chr   pos      lod  ci_lo  ci_hi
1        1 HB.Novel.Entries  18 21.29 6.400137 21.017 21.893

  lodindex         lodcolumn chr    pos      lod  ci_lo  ci_hi
1        1 HB.Repeat.Entries   2 48.993 8.743605 48.974 49.042

  lodindex                                         lodcolumn chr    pos
1        1 NPP.NoveltyPreference.ZoneTime_WhiteVsBlack_Total   9 14.308
       lod  ci_lo  ci_hi
1 6.497207 11.625 14.321

  lodindex                                           lodcolumn chr   pos
1        1 NPP.NoveltyPreference.ZoneTime_GreyWhiteBlack_Total   5 3.515
       lod ci_lo ci_hi
1 6.573749 3.164 3.833

dev.off()

png 
  2

for(i in names(condi.m2.qtl.out)){
  print(i)
  if(is.null(condi.m2.snps[[i]]))
   next
  top_1 <- data.frame(pheno = i)
  top <- top_snps(condi.m2.snps[[i]]$lod, condi.m2.snps[[i]]$snpinfo)
  top <- cbind(top_1, top)
  write.table(top, file = "output/conditional.Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", sep = ",",
              row.names = F, col.names = T, append = TRUE)
  
  topgene <- cbind(top_1, condi.m2.genes[[i]])
  write.table(topgene, file = "output/conditional.Novelty_residuals_RankNormal_datarelease_12182019-genelist.csv", sep = ",",
              row.names = F, col.names = T, append = TRUE)
}

[1] "OFA.total.distance.traveled"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(topgene, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
genelist.csv", : appending column names to file

[1] "OFA.distance.traveled.slope"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.total.time.in.corner"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.total.time.in.perimeter"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.total.time.in.center"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.total.ambulatory.time"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.total.distance.traveled.in.perimeter"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.total.distance.traveled.in.center"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.total.distance.traveled.in.corner"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.pct.dist.center"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.pct.dist.corner"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.pct.dist.perimeter"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.pct.time.center"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.pct.time.corner"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.pct.time.perimeter"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.distance.traveled.first.five"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "OFA.distance.traveled.last.five"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "LD.pct.distance.traveled.in.light"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "LD.pct.ambulatory.time.in.light"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "LD.pct.resting.time.in.light"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "LD.pct.time.in.light"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "LD.pct.ambulatory.Counts.in.light"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "LD.total.transitions"
[1] "HB.Total.Entries"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "HB.Novel.Entries"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "HB.Repeat.Entries"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "NPP.NoveltyPreference.ZoneTime_WhiteVsBlack_Total"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

[1] "NPP.NoveltyPreference.ZoneTime_GreyWhiteBlack_Total"

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

Warning in write.table(top, file = "output/
conditional.Novelty_residuals_RankNormal_datarelease_12182019-
variantlist.csv", : appending column names to file

sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)

locale:
[1] C

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

other attached packages:
[1] ggplot2_3.1.0 qtl2_0.18    

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2        pillar_1.3.1      git2r_0.23.0     
 [4] plyr_1.8.4        workflowr_1.4.0   tools_3.3.2      
 [7] digest_0.6.18     bit_1.1-14        RSQLite_2.1.1    
[10] evaluate_0.10     memoise_1.1.0     tibble_2.1.3     
[13] gtable_0.2.0      pkgconfig_2.0.1   rlang_0.4.0      
[16] DBI_1.0.0         yaml_2.2.0        parallel_3.3.2   
[19] withr_2.1.2       stringr_1.3.1     dplyr_0.8.3      
[22] knitr_1.20        fs_1.2.6          rprojroot_1.3-2  
[25] bit64_0.9-7       grid_3.3.2        tidyselect_0.2.5 
[28] glue_1.3.1        data.table_1.11.4 R6_2.4.0         
[31] rmarkdown_1.11    purrr_0.3.2       blob_1.1.1       
[34] magrittr_1.5      whisker_0.3-2     backports_1.1.2  
[37] scales_1.0.0      htmltools_0.3.6   assertthat_0.2.1 
[40] colorspace_1.4-0  stringi_1.2.4     lazyeval_0.2.1   
[43] munsell_0.5.0     crayon_1.3.4

plot_conditional_m2.Novelty_residuals_RankNormal_datarelease_12182019

Hao He

2020-02-25

plot scan result for conditional_m2.Novelty_residuals_RankNormal_datarelease_12182019