Annotate GWAS / QTL signals using bed4 format table object that provided by user — xQTLanno_chippeak • xQTLbiolinks

Annotate GWAS / QTL signals using bed4 format table object that provided by user

xQTLanno_chippeak(
  snpInfo = "",
  genomeVersion = "hg38",
  enrichElement = NULL,
  distLimit = 1
)

Arguments

snpInfo: A data.table/data.frame with three columns: chromosome, position and p-value.
genomeVersion: "hg38" (default) or "hg19". Note: hg19 will be converted to hg38 automatically.
enrichElement: A data.table of data.frame object including 4 columns (consistent with bed4 format): chrom, start, end, name.
distLimit: Defaults: 0 (variants overlap with elements).

Value

A data.table object

Examples

# \donttest{
url1 <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/gwas/gwasSub.txt.gz"
url2 <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/enhancer.txt"
snpInfo <- data.table::fread(url1, sep="\t")
enhancerDT <- data.table::fread(url2, sep="\t")
variants_hit_enhancer <- xQTLanno_chippeak(snpInfo, enrichElement=enhancerDT)
# }