wrapper_getGEO: Wrapper of the GEOquery::getGEO() function

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

Wrapper of the GEOquery::getGEO() function

Description

The wrapper function adds some basic validity checks including format of the study identifier and number of different platforms used in the study.

Usage

wrapper_getGEO(
  gse,
  GSEMatrix = TRUE,
  AnnotGPL = FALSE,
  getGPL = FALSE,
  platform = NULL,
  temp.dir = tempdir()
)

Details

This functions results in an error if the study identifier does not start with GSE and if more than one platform is used in a study. If the latter is the case, the desired platform can be set using the platform parameter.

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