Last updated: 2020-01-09

Checks: 2 0

Knit directory: csna_workflow/

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Unstaged changes:
    Modified:   README.md
    Modified:   _workflowr.yml
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    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/08_gcta_herit.R
    Modified:   analysis/09_qtlmapping.R
    Modified:   analysis/10_qtl_permu.R
    Modified:   analysis/11_qtl_blup.R
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    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_08_gcta_herit.R
    Modified:   analysis/run_09_qtlmapping.R
    Modified:   analysis/run_10_qtl_permu.R
    Modified:   analysis/run_11_qtl_blup.R

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1 Data transformation from Finalreport.txt to qtl2 for 11 batches of Jackson_Lab_Bubier

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 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