variant enrichment analysis — xQTLanalyze_enrich • xQTLbiolinks

variant enrichment analysis

xQTLanalyze_enrich(
  snpInfo = "",
  genomeVersion = "hg38",
  enrichElement = "Promoter",
  distLimit = 1e+06
)

Arguments

snpInfo: A data.table/data.frame with two or three columns: chromosome and position.
genomeVersion: "hg38" (default) or "hg19". Note: hg19 will be converted to hg38 automatically.
enrichElement: "Promoter", "Enhancer" or "TF".
distLimit: Defaults: 1e6

Value

A data.table object

Examples

# \donttest{
url1 <- "https://github.com/dingruofan/exampleData/raw/master/gwas/gwasSub.txt.gz"
snpInfo <- data.table::fread(url1, sep="\t")
enrichHits <- xQTLanalyze_enrich(snpInfo,enrichElement="Enhancer")
# }