xQTLbiolinks (version 1.6.2)

xQTLanalyze_coloc: 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
)

Value

A list of coloc result and details.

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.

Examples

# \donttest{
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")
# }