xQTLquery_eqtlSig | R Documentation |
Query significant eQTL associations for a specified tissue or multiple tissues.
xQTLquery_eqtlSig(
variantName = "",
genes = "",
variantType = "auto",
geneType = "auto",
tissueSiteDetail = ""
)
variantName |
(character) name of variant, dbsnp ID and variant id is supported, eg. "rs138420351" and "chr17_7796745_C_T_b38". |
genes |
(character string or a character vector) gene symbols or gencode ids (versioned or unversioned are both supported). |
variantType |
(character) options: "auto", "snpId" or "variantId". Default: "auto". |
geneType |
(character) options: "auto","geneSymbol" or "gencodeId". Default: "auto". |
tissueSiteDetail |
(character) details of tissues in GTEx can be listed using |
A data.table object.
# Query significant eQTL associations with a variant id across all tissues:
xQTLquery_eqtlSig("rs201327123")
xQTLquery_eqtlSig("chr1_14677_G_A_b38")
# Query significant eQTL associations with a variant id in a specified tissue:
xQTLquery_eqtlSig("chr1_14677_G_A_b38",
tissueSiteDetail="Skin - Sun Exposed (Lower leg)")
# Query eQTL associations for multiple variants:
varInfo <- xQTLquery_varPos(chrom="chr1", pos=c(1102708))
xQTLquery_eqtlSig(variantName=varInfo$snpId)
# Query eQTL associations by genes or tissues:
xQTLquery_eqtlSig(genes="ATAD3B")
xQTLquery_eqtlSig(genes=c("TP53", "SLC35E2B"), tissueSiteDetail= "Brain - Cerebellum")
xQTLquery_eqtlSig(genes="ENSG00000141510.16")
# Query eQTL associations with a variant-gene pair:
xQTLquery_eqtlSig(variantName="rs1641513", genes="TP53")
xQTLquery_eqtlSig(variantName="chr1_1667948_A_G_b38",
genes="SLC35E2B", tissueSiteDetail="Kidney - Cortex")
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