Genomic annotation of significant signals from GWAS / QTL — xQTLanno_genomic • xQTLbiolinks

Genomic annotation of significant signals from GWAS / QTL

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

# \donttest{
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)
# }