Last updated: 2020-02-19

Checks: 2 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.

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Repository version: f28221a

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    Modified:   analysis/run_09_qtlmapping.R
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    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