index.Rmd

---
title: "CSNA_workflow"
author: "Hao He"
site: workflowr::wflow_site
output:
  workflowr::wflow_html:
    toc: true
---

### 1 Data transformation from Finalreport.txt to qtl2 for 12 batches
* [01_FinalReport2qtl2.R]

### 2 Grab intensities from GeneSeek FinalReport.txt files convert them to a single big data frame
* [02_FinalReport2intensity.R]

### 3 First time to calculate genoprobs, maxmarg, crossover, errorlod, snpg for the qc diagnositics
* [03_firstgm2genoprobs.R]

### 4 Genotype diagnostics for diversity outbred mice of 12 batches
* [04_diagnosis_qc_gigamuga_nine_batches.Rmd](04_diagnosis_qc_gigamuga_nine_batches.html)
* [04_diagnosis_qc_gigamuga_11_batches.Rmd](04_diagnosis_qc_gigamuga_11_batches.html)

### 5 After QC, genotype diagnostics
* [05_after_diagnosis_qc_gigamuga_nine_batches.Rmd](05_after_diagnosis_qc_gigamuga_nine_batches.html)
* [05_after_diagnosis_qc_gigamuga_11_batches.Rmd](05_after_diagnosis_qc_gigamuga_11_batches.html)

### 6 Calculation of the genoprobs after qc and do interpolatino to 69K grid
* [06_final_pr_apr_69K.R]

### 7 Plot the recombination block size and founder props across all generations
* [07_recomb_size_founder_prop.Rmd](07_recomb_size_founder_prop.html)

### 8 GCTA heritability 
* [08_gcta_herit.R]

### 9 qtl mapping
* [09_qtlmapping.R]

### 10 qtl permutation
* [10_qtl_permu.R]

### 11 qtl blup
* [11_qtl_blup.R]

### 12 plot qtl mapping
* [12_plot_qtl_mapping_1.Rmd](12_plot_qtl_mapping_1.html)
* [12_plot_qtl_mapping_2.Rmd](12_plot_qtl_mapping_2.html)
* [12_plot_69k_qtl_mapping_2.Rmd](12_plot_69k_qtl_mapping_2.html)

### 13 conditional_m2_qtlmapping
* [13_conditional_m2_qtlmapping.R]
* [13_plot_conditional_m2_qtlmapping.Rmd](13_plot_conditional_m2_qtlmapping.html)

### 14 geneseek2qtl2fst_Gagnon
* [14_geneseek2qtl2fst_Gagnon.R]

### 15 firstgm2genoprobs_Gagnon
* [15_firstgm2genoprobs_Gagnon.R]

### 16 diagnosis_qc_gigamuga_gagnon
* [16_diagnosis_qc_gigamuga_gagnon.Rmd](16_diagnosis_qc_gigamuga_gagnon.html)