Download significant eQTL associations of a specified tissue or across all tissues.

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

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

Value

A data.table object.

Examples

# \donttest{
# Download eQTL info for a variant:
xQTLdownload_eqtlSig("rs201327123")
xQTLdownload_eqtlSig("chr1_14677_G_A_b38")
xQTLdownload_eqtlSig("chr1_14677_G_A_b38",
                    tissueSiteDetail="Skin - Sun Exposed (Lower leg)")

# Download eQTL association according to all tissues with genome location:
varInfo <-  xQTLquery_varPos(chrom="chr1", pos=c(1102708))
xQTLdownload_eqtlSig(variantName=varInfo$snpId)

# Download eQTL info for gene:
xQTLdownload_eqtlSig(genes="ATAD3B")
xQTLdownload_eqtlSig(genes=c("TP53", "SLC35E2B"), tissueSiteDetail= "Brain - Cerebellum")
xQTLdownload_eqtlSig(genes="ENSG00000141510.16")

# Download eQTL info for a variant-gene pair:
xQTLdownload_eqtlSig(variantName="rs1641513", genes="TP53")
xQTLdownload_eqtlSig(variantName="chr1_1667948_A_G_b38",
                     genes="SLC35E2B", tissueSiteDetail="Kidney - Cortex")
# }