extract_pheno_data: Extract phenotype data

In szymczak-lab/harmonizeGeneExprData: Harmonization of gene expression data from GEO and ArrayExpress

Extract phenotype data

Description

Extract phenotype data from GEO or ArrayExpress depending on study identifier.

Usage

extract_pheno_data(study.id, temp.dir = tempdir(), platform = NULL)

Arguments

study.id	[character(1)] study identifier (GSEXXX for GEO, E-MTAB-XXX for ArrayExpress)
temp.dir	[character(1)] directory where temporary files should be stored
platform	[character(1)] platform to be selected in GEO studies which use several platforms

Details

All phenotype data available at GEO or ArrayExpress is returned without any modifications.

Value

[data.frame] phenotype data for each sample and all variables provided by GEO or ArrayExpress

Examples

study.id = "GSE67785"
pheno.original = extract_pheno_data(
  study.id = study.id)

szymczak-lab/harmonizeGeneExprData documentation built on Dec. 1, 2022, 9:07 p.m.