xQTLdownload_eqtlAllAssoPos: Download summary statistics data for eQTLs with genome...

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

Download summary statistics data for eQTLs with genome positions.

Description

Download summary statistics data for eQTLs with genome positions.

Usage

xQTLdownload_eqtlAllAssoPos(
  chrom = "",
  pos_lower = numeric(0),
  pos_upper = numeric(0),
  p_lower = 0,
  p_upper = 1.1,
  gene = "",
  geneType = "auto",
  tissueLabel = "",
  study = "gtex_v8",
  recordPerChunk = 1000,
  withB37VariantId = FALSE
)

Arguments

chrom	(character) name of chromesome, including chr1-chr22, chrX.
pos_lower	(integer) lower base pair location threshold, expressed as an integer
pos_upper	(integer) upper base pair location threshold, expressed as an integer
p_lower	(numeric) lower p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
p_upper	(numeric) upper p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
gene	(character) gene symbol or gencode id (versioned or unversioned are both supported).
geneType	(character) options: "auto","geneSymbol" or "gencodeId". 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".
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.

Value

A data.table object

Examples

eqtlAssos <- xQTLdownload_eqtlAllAssoPos(chrom = "chr11",
                                        pos_lower=101400000, pos_upper = 101400013,
                                        tissueLabel="Brain - Cerebellar Hemisphere",
                                        )

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