xQTLdownload_eqtlExp: Download normalized expression for gene with a variant-gene...

In xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

Download normalized expression for gene with a variant-gene pair

Description

Download normalized expression for gene with a variant-gene pair

Usage

xQTLdownload_eqtlExp(
  variantName = "",
  gene = "",
  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".
gene	(character) 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

Value

A data.table object.

Examples

# Download exp with variant-gene pair in different tissues:
xQTLdownload_eqtlExp(variantName="rs1641513",gene="TP53", tissueSiteDetail="Liver")

# Download expression using variant ID and gencode ID.
xQTLdownload_eqtlExp(variantName="chr1_14677_G_A_b38",gene="ENSG00000228463.9",
                     tissueSiteDetail="Stomach")

xQTLbiolinks documentation built on Sept. 15, 2023, 1:06 a.m.