xQTLbiolinks (version 1.6.2)

xQTLquery_eqtl: Query multi-tissue eQTL metasoft results

Description

can be quried with a gene/variant-gene pair.

Usage

xQTLquery_eqtl(
  variantName = "",
  gene = "",
  variantType = "auto",
  geneType = "auto",
  tissueSiteDetail = "",
  recordPerChunk = 100
)

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".

gene

(character) gene symbol or gencode id (versioned or unversioned are both supported). Can not be null.

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

recordPerChunk

(integer) number of records fetched per request (default: 100).

Examples

# \donttest{
# Query with a gene symbol:
eqtlInfo <- xQTLquery_eqtl(gene="TP53")

# Query with unversioned gencode ID:
eqtl_v8 <- xQTLquery_eqtl(gene="ENSG00000141510")

# In a specific tissue:
xQTLquery_eqtl(gene="ENSG00000141510", geneType="gencodeId",  tissueSiteDetail="Thyroid" )

# Query with a variant-gene pair:
xQTLquery_eqtl(variantName="rs1641513",gene="TP53")
xQTLquery_eqtl(variantName="chr1_1667948_A_G_b38", gene="SLC35E2B",
                  tissueSiteDetail="Kidney - Cortex")
# }