xQTLanalyze_coloc: Conduct colocalization analysis with trait genes generated...

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

Conduct colocalization analysis with trait genes generated from xQTLanalyze_getTraits

Description

Conduct colocalization analysis with trait genes generated from xQTLanalyze_getTraits

Usage

xQTLanalyze_coloc(
  gwasDF,
  traitGene,
  geneType = "auto",
  genomeVersion = "grch38",
  tissueSiteDetail = "",
  study = "gtex_v8",
  mafThreshold = 0.01,
  population = "EUR",
  gwasSampleNum = 50000,
  method = "coloc",
  token = "9246d2db7917",
  bb.alg = FALSE
)

Arguments

gwasDF	A data.frame or data.table objectof gwas.
traitGene	A gene symbol or a gencode id (versioned).
geneType	(character) options: "auto","geneSymbol" or "gencodeId". Default: "auto".
genomeVersion	"grch38" (default) or "grch37". Note: grch37 will be converted to grch38 automatically.
tissueSiteDetail	(character) details of tissues in GTEx can be listed using tissueSiteDetailGTExv8 or tissueSiteDetailGTExv7
study	(character) name of studies can be listed using "ebi_study_tissues"
mafThreshold	Cutoff of maf to remove rare variants.
population	Supported population is consistent with the LDlink, which can be listed using function "LDlinkR::list_pop()"
gwasSampleNum	Sample number of GWAS dataset. Default:50000.
method	(character) options: "coloc"(default) or "hyprcoloc" (must be updated to the latest version from the github to use hyprcoloc ). Package coloc or hyprcoloc is required.
token	LDlink provided user token, default = NULL, register for token at https://ldlink.nci.nih.gov/?tab=apiaccess
bb.alg	For hyprcoloc, branch and bound algorithm: TRUE, employ BB algorithm; FALSE, do not. Default: FALSE.

Value

A list of coloc result and details.

Examples

url1 <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/gwasDFsub_MMP7.txt"
gwasDF <- data.table::fread(url1)
output <- xQTLanalyze_coloc(gwasDF = gwasDF, traitGene= "MMP7", tissueSiteDetail="Prostate")

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