xQTLbiolinks (version 1.6.2)

xQTLquery_eqtlSig: Query significant eQTL associations for a specified tissue or multiple tissues.

Description

Query significant eQTL associations for a specified tissue or multiple tissues.

Usage

xQTLquery_eqtlSig(
  variantName = "",
  genes = "",
  variantType = "auto",
  geneType = "auto",
  tissueSiteDetail = ""
)

Value

A data.table object.

Arguments

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 tissueSiteDetailGTExv8 or tissueSiteDetailGTExv7

Examples

# \donttest{
# 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")
# }