importExpressionDataGEO: Import expression data and probe mappings from GEO dataset

In bhatturam/prius: Affected pathway ranking in differential gene expression analysis

Description

This function processes the expression set and gpl files obtained using the GEOQuery package

Usage

importExpressionDataGEO(eset, gpl, selectorFunction = probeSelectorATSAT,
  combinerFunction = probeCombinerMean)

Arguments

eset	An expression set, for more details refer to https://www.bioconductor.org/packages/3.3/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf and http://svitsrv25.epfl.ch/R-doc/library/GEOquery/html/GDS2MA.html
gpl	GEO Platform entity, refer http://svitsrv25.epfl.ch/R-doc/library/GEOquery/html/GPL-class.html for more details
selectorFunction	a function that accepts a probeName string and returns true if the probe is to be considered. See probeSelectorATSAT for an example.
combinerFunction	a function that accepts a comma separated string and returns true if the probe is to be considered. See probeCombinerMean for an example.

Value

A data frame with columns as sample names, and rows containing the expression values of each as HGNC Symbol.

Examples

## Not run: 
library(GEOquery)
data_folder = tempdir()
gds = getGEO('GDS3837',AnnotGPL = TRUE, getGPL = TRUE,destdir = data_folder)
gpl = getGEO(Meta(gds)$platform,destdir = data_folder)
eset = GDS2eSet(gds, GPL=gpl,do.log2=FALSE)
gdata=importExpressionDataGEO(eset,gpl)

## End(Not run)

bhatturam/prius documentation built on May 12, 2019, 8:24 p.m.