xQTLanalyze_coloc_diy: Conduct colocalization analysis with customized QTL data

In xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

Conduct colocalization analysis with customized QTL data

Description

Conduct colocalization analysis with customized QTL data

Usage

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

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")

xQTLbiolinks documentation built on Sept. 15, 2023, 1:06 a.m.