get_geo_data: Export gene expression data sets from GEO

In szymczak-lab/QCnormSE: Quality Control of Normalized Gene Expression Data

Export gene expression data sets from GEO

Description

Downloads normalized gene expression data from Gene Expression Omnibus (GEO) and stores it as a SummarizedExperiment object. Information about detection P values and dates of scanning can also be extracted.

Usage

get_geo_data(
  accession,
  temp.dir = tempdir(),
  platform = NULL,
  detection.pvalue = FALSE,
  scan.date = FALSE
)

Arguments

accession	Character. Identifier of GEO data set (GSEXXX).
temp.dir	Character. Destination directory to downloaded array files.
platform	Character. GEO identifier of platform that should be selected. Only relevant, if study profiled samples on different platforms.
detection.pvalue	Logical. Should information about detection P values be extracted (if available)?
scan.date	Logical. Should information about scan dates be extracted (if raw data files are available)?

Value

RangedSummarizedExperiment-class object.

Examples

se = get_geo_data(accession = "GSE6710")

szymczak-lab/QCnormSE documentation built on March 25, 2023, 1:05 p.m.