Buck9195/Gladstone-Bioinformatics-Workshop
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MichelaTr 2023-11-24 11:35:35 -08:00 • committed by GitHub
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2 changed files with 13 additions and 5 deletions
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3
GWAS_PRS/scripts/step03_plink_GWAS.sh
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@ -2,6 +2,7 @@
#GWAS
########################################################################
plink_dir=~/Desktop/handson_plink
cd ~/Desktop/handson_plink/GWAS
mkdir plink_results/
#linear model --glm or --linear
#no covariates
@ -31,7 +32,7 @@ $plink_dir/plink2 --pfile genotypes/unrelated_hg38_auto_maf_0.05_500k_snp_filter
#logistic model --glm or --logistic
$plink_dir/plink2 --1 --pfile genotypes/unrelated_hg38_auto_maf_0.05_500k_snp_filtered \
--covar covariates/covariates_with_10PCs.csv --covar-variance-standardize \
--glm omit-ref cols=+beta,+orbeta,+ci hide-covar \
--glm omit-ref cols=+orbeta,+ci hide-covar \
--pheno phenotypes/phenofile.csv --pheno-name obesity --ci 0.95 \
--out plink_results/sex.age.PCs.adj

15
GWAS_PRS/scripts/step04_GWAS_visualization.R
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@ -3,7 +3,7 @@
#Visualization in R
##################
#manhattan plot
install.packages("qqman")
#install.packages("qqman")
library(qqman)
setwd("~/Desktop/handson_plink/GWAS/")
@ -44,15 +44,22 @@ qq(gwas_BMI_sex_age_adj$P, main="quantile-quantile plot - sex, age adjusted BMI"
qq(gwas_BMI_sex_age_PCs_adj$P, main="quantile-quantile plot - sex, age, PCs adjusted BMI")
dev.off()
#include
#pvals <- read.table("AMH_all_FVG_rs_pvalue", header=T)
#observed <- sort(pvals$pgc)
#alternative to calculate x and y axes for qqplot
#observed <- sort(gwas_obesity$P)
#lobs <- -(log10(observed))
#expected <- c(1:length(observed))
#lexp <- -(log10(expected / (length(expected)+1)))
#pdf("R_plots/obesity_qqplot.pdf", width=480, height=480)
#plot(c(0,8), c(0,8), col="red", lwd=3, type="l", xlab="Expected (-logP)", ylab="Observed (-logP)", main="quantile-quantile plot - sex, age, PCs adjusted obesity", xlim=c(0,8), ylim=c(0,8), las=1, xaxs="i", yaxs="i", bty="l")
#points(lexp, lobs, pch=23, cex=.4, bg="black")
#dev.off()
########################################################################
#open and run step05_Plink_PRS.sh