TD_GWAS

This directory contains course materials for TD GWAS.

Required Softwares

• R version 4.0.3 (https://pbil.univ-lyon1.fr/CRAN/)
• Rstudio version 1.3 (https://rstudio.com/products/rstudio/download/)
• PLINK version 1.90 beta (https://www.cog-genomics.org/plink2)

Required R Packages

• dplyr, tidyr, scales, data.table, ggplot2

Toy Data

The toy data is a subset of the freely HapMap data, containing only CEU samples, a binary trait was simulated for only founders.

Can be downloaded here: https://share-good.egid.fr/fop/VZfxQvAD/TD_GWAS_data.zip

• Raw HapMap CEU samples PLINK format data (build 36): hapmap_ceu.bim, hapmap_ceu.bed, hapmap_ceu.fam
• Samples included in population structure check: hapmap_1kg.fam, hapmap_ceu_pca_1kg_adj_clean.fam
• PCA eigenvalues and eigenvector for population structure check: hapmap_1kg.eigenval, hapmap_1kg.eigenvec
• Covariables sex, PC1 and PC2: covars.txt
• Logistic regression results: res_glm_covar_chr22.assoc.logistic
• Some R functions for data visualization: viz_functions.R
• Temporary file for figures: figs/
• TD supports: TD_GWAS.Rmd and TD_GWAS.html
• HapMap sample population: relationships_w_pops_041510.txt (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/20100804.ALL.panel)
• 1,000 genomes population: 20100804.ALL.panel (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/20100804.ALL.panel)
• 1,000 genomes population and super-population: integrated_call_samples_v3.20130502.ALL.panel (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel)

HapMap CEU Sample Extraction

The CEU samples were extracted using following commands:

## HapMap plink format data
wget https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/hapmap3_r3/plink_format/hapmap3_r3_b36_fwd.consensus.qc.poly.map.gz
wget https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/hapmap3_r3/plink_format/hapmap3_r3_b36_fwd.consensus.qc.poly.ped.gz
gunzip hapmap3_r3_b36_fwd.consensus.qc.poly.ped.gz
gunzip hapmap3_r3_b36_fwd.consensus.qc.poly.map.gz

## HapMap phenotype
wget https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/hapmap3_r3/relationships_w_pops_041510.txt
awk '($7=="CEU") {print$1,$2}' relationships_w_pops_041510.txt > hapmap_ceu_sample.txt

## Extraction
plink1.9 --file hapmap3_r3_b36_fwd.consensus.qc.poly --keep hapmap_ceu_sample.txt --make-bed --out hapmap_ceu

## Binary trait simulation
pop <- data.table::fread("relationships_w_pops_041510.txt", header = TRUE)[population == "CEU", ]
set.seed(20201106)
sim_trait <- sample(1:2, size = nrow(pop[dad == mom]), prob = c(2/3, 1/3), replace = TRUE)
fam_trait <- pop[, 1:5][dad == mom, pheno := sim_trait]
fam_trait$pheno[is.na(fam_trait$pheno)] <- -9
write.table(
  fam_trait, 
  file = "hapmap_ceu.fam", 
  sep = "\t", 
  col.names = FALSE, 
  row.names = FALSE,
  quote = FALSE
)