Conduct colocalization analysis with customized QTL data

Conduct colocalization analysis with customized QTL data

xQTLanalyze_coloc_diy(
  gwasDF,
  qtlDF,
  mafThreshold = 0.01,
  gwasSampleNum = 50000,
  qtlSampleNum = 10000,
  method = "coloc",
  bb.alg = FALSE
)

Arguments

gwasDF

data.frame or data.table, required cols: rsid, chrom, position, pValue, maf, beta, se

qtlDF

data.frame or data.table, required cols: rsid, chrom, position, pValue, maf, beta, se

mafThreshold

Cutoff of maf to remove rare variants.

gwasSampleNum

Sample number of GWAS dataset. Default:50000.

qtlSampleNum

Sample number of QTL dataset. Default:10000.

method

(character) options: "coloc"(default) or "hyprcoloc" (need a highe version).

bb.alg

For hyprcoloc, branch and bound algorithm: TRUE, employ BB algorithm; FALSE, do not. Default: FALSE.

Value

A list

Examples

# \donttest{
url1 <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/gwasDFsub_MMP7.txt"
url2 <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/eqtl/MMP7_qtlDF.txt"
gwasDF <- data.table::fread(url1)
qtlDF <- data.table::fread(url2)
output <- xQTLanalyze_coloc_diy(gwasDF = gwasDF, qtlDF=qtlDF, method="coloc")
# }