xQTLdownload_exp: Download normalized gene expression at the sample level for a...

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

Download normalized gene expression at the sample level for a specified tissue.

Description

Download normalized gene expression at the sample level for a specified tissue.

Usage

xQTLdownload_exp(
  genes = "",
  geneType = "auto",
  tissueSiteDetail = "Liver",
  toSummarizedExperiment = FALSE,
  recordPerChunk = 80,
  pathologyNotesCategories = FALSE
)

Arguments

genes	(character string or a character vector) gene symbols or gencode ids (versioned or unversioned are both supported).
geneType	(character) options: "auto","geneSymbol" or "gencodeId". Default: "auto".
tissueSiteDetail	(character) details of tissues in GTEx can be listed using tissueSiteDetailGTExv8 or tissueSiteDetailGTExv7
toSummarizedExperiment	a logical value indicating whether to return a data.frame or a summarizedExperiment object. Default: TRUE, return a toSummarizedExperiment object.
recordPerChunk	(integer) number of records fetched per request (default: 80).
pathologyNotesCategories	a logical value indicating whether to return pathologyNotes. Default: FALSE, the pathologyNotes is ignored.

Value

return a SummarizedExperiment or a data.table object harbing gene expression profiles and samples' information.

Examples

# Download gene expression with a genecode ID:
expProfiles <- xQTLdownload_exp("ENSG00000210195.2", tissueSiteDetail="Liver")

# Download gene expression into a SummarizedExperiment object:
expProfiles <- xQTLdownload_exp("ENSG00000210195.2", tissueSiteDetail="Liver",
               toSummarizedExperiment=TRUE)
# extract expression profile from SummarizedExperiment object:
expDT <- SummarizedExperiment::assay(expProfiles)
# extract samples' detail from SummarizedExperiment object:
sampleDT <- SummarizedExperiment::colData(expProfiles)

# Download gene expression profiles of multiple genes:
expProfiles <- xQTLdownload_exp(c("tp53","naDK","SDF4"),
                                tissueSiteDetail="Artery - Coronary",
                                pathologyNotesCategories=TRUE)

# Download with versioned and unversioned gencode Id.
expProfiles <- xQTLdownload_exp(c("ENSG00000141510.16","ENSG00000008130.15","ENSG00000078808"),
                               tissueSiteDetail="Artery - Coronary")

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