xQTLanno_chippeak | R Documentation |
enrichment analysis for GWAS / QTL signals in functional elements, including enhancer, promoter, CPG, and TFs
xQTLanno_chippeak(
snpInfo = "",
genomeVersion = "hg38",
enrichElement = NULL,
distLimit = 1
)
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). |
A data.table object
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)
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