writeExprsGEO: Return and write gene expression values for GEO

In peterjuv/FunGenPipe: Tools for building function genomics pipelines

Description

Downloads platform info file from GEO using GPL accession number gplAccNum. Adds platform IDs that are missing from ExpressionSet esetAnn and sets their values to NA. Writes data to tad-delimited file filePath if specified. Uses rownames(esetAnn) as IDs.

Usage

writeExprsGEO(esetAnn, gplAccNum, filePath = NULL, remGPL = TRUE, ...)

Arguments

esetAnn	ExpressionSet
gplAccNum	Character GEO GPL accession number
filePath	Character path/fileName.txt; default NULL
remGPL	Delete the downloaded GPL*.soft file; default TRUE
...	Further arguments passed to GEOquery::getGEO(...)

Value

Matrix expression values for GEO.

peterjuv/FunGenPipe documentation built on June 18, 2021, 3:38 a.m.