xQTLanalyze_getTraits
R/analyze.R
xQTLanalyze_coloc.Rd
Conduct colocalization analysis with trait genes generated from xQTLanalyze_getTraits
xQTLanalyze_coloc(
gwasDF,
traitGene,
geneType = "auto",
genomeVersion = "grch38",
tissueSiteDetail = "",
study = "gtex_v8",
mafThreshold = 0.01,
population = "EUR",
gwasSampleNum = 50000,
method = "coloc",
data_source = "liLab",
token = "9246d2db7917",
bb.alg = FALSE
)
A data.frame or data.table objectof gwas.
A gene symbol or a gencode id (versioned).
(character) options: "auto","geneSymbol" or "gencodeId". Default: "auto".
"grch38" (default) or "grch37". Note: grch37 will be converted to grch38 automatically.
(character) details of tissues in GTEx can be listed using tissueSiteDetailGTExv8
or tissueSiteDetailGTExv7
(character) name of studies can be listed using "ebi_study_tissues"
Cutoff of maf to remove rare variants.
Supported population is consistent with the LDlink, which can be listed using function "LDlinkR::list_pop()"
Sample number of GWAS dataset. Default:50000.
(character) options: "coloc"(default) or "hyprcoloc". Package coloc
or hyprcoloc
is required.
"eQTL_catalogue" or "liLab" (default)
LDlink provided user token, default = NULL, register for token at https://ldlink.nci.nih.gov/?tab=apiaccess
For hyprcoloc
, branch and bound algorithm: TRUE, employ BB algorithm; FALSE, do not. Default: FALSE.
A list of coloc result and details.
# \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")
# }