index.Rmd

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

### 0 Process all phenotypes in founder CC and DO
* [00_Process_all_phenotypes_in_founder_CC_DO.Rmd](00_Process_all_phenotypes_in_founder_CC_DO.html)

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

### 2 Grab intensities from GeneSeek FinalReport.txt files
* [analysis/scripts/02_FinalReport2intensity.R]

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

### 4 Genotype diagnostics for diversity outbred mice of 12 batches
* [04_diagnosis_qc_gigamuga_12_batches.Rmd](04_diagnosis_qc_gigamuga_12_batches.html)
* [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_12_batches.Rmd](05_after_diagnosis_qc_gigamuga_12_batches.html)
* [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
* [analysis/scripts/06_final_pr_apr_69K.R]

### 7 DO Diversity Report
* [analysis/scripts/07_do_diversity_report.R]
* [07_do_diversity_report.Rmd](07_do_diversity_report.html)

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