In MRCIEU/gwasvcf: Tools for Dealing with GWAS Summary Data in VCF Format

Setup

library(knitr)
opts_chunk$set(warning=FALSE, message=FALSE, cache=TRUE)
library(devtools)
load_all()
fn <- system.file("data","IEU-a-2.vcf.gz", package="gwasvcftools")
chrompos <- "20:800000-4000000"
pval <- 5e-8
rsid <- c("rs3128126", "rs3121561", "rs3813193")

Reading in the vcf file

system.time({
    v <- readVcf(fn)
})

Different methods for searching for rsid:

system.time({
    query_rsid_vcf(rsid, v)
})
system.time({
    query_rsid_file(rsid, fn)
})
system.time({
    query_rsid_bcftools(rsid, fn)
})

Different methods for searching by p-value:

system.time({
    query_pval_vcf(pval, v)
})
system.time({
    query_pval_file(pval, fn)
})
system.time({
    query_pval_bcftools(pval, fn)
})

Different methods for searching by chrompos:

system.time({
    query_chrompos_vcf(chrompos, v)
})
system.time({
    query_chrompos_file(chrompos, fn)
})
system.time({
    query_chrompos_bcftools(chrompos, fn)
})

MRCIEU/gwasvcf documentation built on Sept. 11, 2023, 7:50 p.m.