xQTLdownload_eqtlAllAsso: Download summary statistics data for eQTLs with a specified...

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

Download summary statistics data for eQTLs with a specified gene, variant, tissue or study

Description

source of all eQTL associations is EBI eQTL category.

Usage

xQTLdownload_eqtlAllAsso(
  gene = "",
  geneType = "auto",
  variantName = "",
  variantType = "auto",
  tissueLabel = "",
  study = "",
  recordPerChunk = 1000,
  withB37VariantId = FALSE,
  data_source = "eQTL_catalogue",
  API_version = "v1"
)

Arguments

gene	(character) gene symbol or gencode id (versioned or unversioned are both supported).
geneType	(character) options: "auto","geneSymbol" or "gencodeId". Default: "auto".
variantName	(character) name of variant, dbsnp ID and variant id is supported, eg. "rs138420351" and "chr17_7796745_C_T_b38".
variantType	(character) options: "auto", "snpId" or "variantId". Default: "auto".
tissueLabel	(character) all supported tissues can be listed using "ebi_study_tissues"
study	(character) name of studies can be listed using "ebi_study_tissues". If the study is null, use all studies (Default).
recordPerChunk	(integer) number of records fetched per request (default: 1000).
withB37VariantId	a logical value indicating whether to return the genome location(GTEx v7) of variants. Default: FALSE.
data_source	"eQTL_catalogue"(default) or "liLab"
API_version	"v1"(default) or "v2"(not working)

Value

A data.table object.

Examples

# Download all eQTL associations of MLH1-rs13315355 pair in all tissues from all studies:
eqtlAsso <- xQTLdownload_eqtlAllAsso(gene="MLH1", variantName = "rs13315355")

# Download eQTL associations of gene ATP11B in CD4+ T cell from all supported studies:
geneAsso <- xQTLdownload_eqtlAllAsso(gene="MMP7",tissueLabel = "CD4+ T cell")

# Download eQTL associations of gene ATP11B in Muscle - Skeletal from GTEx_V8:
geneAsso <- xQTLdownload_eqtlAllAsso("ATP11B", tissueLabel="Muscle - Skeletal")

# Download eQTL associations of SNP rs11568818 in Muscle - Skeletal from GTEx_V8:
varAsso <- xQTLdownload_eqtlAllAsso(variantName="chr11_102530930_T_C_b38",
                                    tissueLabel="Muscle - Skeletal")

# Download all eQTL associations of SNP rs11568818 in all tissues from all supported studies.
varAsso <- xQTLdownload_eqtlAllAsso(variantName="rs11568818")

dingruofan/xQTLbiolinks documentation built on Feb. 12, 2025, 4:57 a.m.