xQTLbiolinks (version 1.6.2)

xQTLdownload_eqtlAllAssoPos: 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
)

Value

A data.table object

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.

Examples

# \donttest{
eqtlAssos <- xQTLdownload_eqtlAllAssoPos(chrom = "chr11",
                                        pos_lower=101398614, pos_upper = 101402313,
                                        tissueLabel="Brain - Cerebellar Hemisphere",
                                        p_upper=1e-1)
# }