xQTLanalyze_getSentinelSnp: Detect sentinel SNPs for GWAS using summary statistics data

In xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

Detect sentinel SNPs for GWAS using summary statistics data

Description

Return sentinel snps whose pValue < 5e-8(default) and SNP-to-SNP distance > 1e6 bp.

Usage

xQTLanalyze_getSentinelSnp(
  gwasDF,
  pValueThreshold = 5e-08,
  centerRange = 1e+06,
  mafThreshold = 0.01,
  genomeVersion = "grch38",
  grch37To38 = FALSE
)

Arguments

gwasDF	A data.frame or a data.table object. Five columns are required (arbitrary column names is supported): ⁠Col 1⁠. "snps" (character), , using an rsID (e.g. "rs11966562"). ⁠Col 2⁠. "chromosome" (character), one of the chromosome from chr1-chr22. ⁠Col 3⁠. "postion" (integer), genome position of snp. ⁠Col 4⁠. "P-value" (numeric). ⁠Col 5⁠. "MAF" (numeric). Allel frequency. ⁠Col 6⁠. "beta" (numeric). effect size. ⁠Col 7⁠. "se" (numeric). standard error.
pValueThreshold	Cutoff of gwas p-value. Default: 5e-8
centerRange	SNP-to-SNP distance. Default:1e6
mafThreshold	Cutoff of maf to remove rare variants.
genomeVersion	Genome version of input file. "grch37" or "grch38" (default).
grch37To38	TRUE or FALSE, we recommend converting grch37 to grch38, or using a input file of grch38 directly. Package rtracklayer is required.

Value

A data.table object.

Examples

url<-"http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/GLGC.txt"
gwasDF <- data.table::fread(url)
gwasDF <- gwasDF[, .(rsid, chr, position, P, maf, beta, se)]
sentinelSnpDF <- xQTLanalyze_getSentinelSnp(gwasDF)

xQTLbiolinks documentation built on Sept. 15, 2023, 1:06 a.m.