xQTLanno_genomic: Genomic annotation of significant signals from GWAS / QTL

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

Genomic annotation of significant signals from GWAS / QTL

Description

Genomic annotation of significant signals from GWAS / QTL

Usage

xQTLanno_genomic(snpInfo = "", p_cutoff = 5e-08, genomeVersion = "hg38")

Arguments

snpInfo	A data.table/data.frame with three columns: chromosome, position, and P-value.
p_cutoff	Cutoff of p-values of significant variants that will be annotated
genomeVersion	"hg38" (default) or "hg19". Note: hg19 will be converted to hg38 automatically.

Value

A data.table object of variants' genomics distribution

Examples

url1 <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/gwas/gwasSub.txt.gz"
snpInfo <- data.table::fread(url1, sep="\t")
snpHits <- xQTLanno_genomic(snpInfo)

dingruofan/xQTLbiolinks documentation built on Feb. 12, 2025, 4:57 a.m.