xQTLbiolinks (version 1.6.2)

xQTLquery_sqtlSig: Query significant sQTL associations for a tissue or multple tissues

Description

Only GTEx v8 is supported.

Usage

xQTLquery_sqtlSig(
  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 symbol or gencode id (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 sQTL associations with rsid:
xQTLquery_sqtlSig(variantName="rs201327123")
xQTLquery_sqtlSig(variantName="chr1_14677_G_A_b38", tissueSiteDetail="Whole Blood")

# Query sQTL associations with gene symbol and gencode ID:
xQTLquery_sqtlSig(genes="ENSG00000141510.16", tissueSiteDetail="Lung" )
xQTLquery_sqtlSig(genes=c("ATAD3B", "MLH1"))

# Query sQTL associations with the variant-genes pair:
xQTLquery_sqtlSig(variantName="rs201327123", genes=c("WASH7P","RP11-206L10.2"))
xQTLquery_sqtlSig(variantName="chr17_7465085_A_G_b38", genes="TP53", tissueSiteDetail="Lung")
# }