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) })
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