xQTLanalyze_coloc_diy | R Documentation |
Conduct colocalization analysis with customized QTL data
xQTLanalyze_coloc_diy(
gwasDF,
qtlDF,
mafThreshold = 0.01,
gwasSampleNum = 50000,
qtlSampleNum = 10000,
method = "coloc",
bb.alg = FALSE
)
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 |
A list
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")
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