runTestOnData: Test expression data

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

Description

Runs the specified test function on the expression data to obtain fold change and p-values.

Usage

runTestOnData(data, normalSampleIndexes, diseaseSampleIndexes, testFunction,
  testFunctionExtraArgs)

Arguments

data	A data frame with columns as sample names, and rows containing the expression values of each as HGNC Symbol. For example the output of importExpressionDataGEO
normalSampleIndexes	The indices of the columns which contain the normal samples
diseaseSampleIndexes	The indices of the columns which contain the disease samples
testFunction	The test function - see logPairedTTestFunction
testFunctionExtraArgs	Extra arguments to the test function

Value

A data frame with as many rows as HGNC Gene Symbols, with the columns defined by the output of testFunction.

Examples

## Not run: 
gds = getGEO('GDS3837',AnnotGPL = TRUE, getGPL = TRUE,destdir = "/tmp")
gpl = getGEO(Meta(gds)$platform,destdir = "/tmp")
eset = GDS2eSet(gds, GPL=gpl,do.log2=FALSE)
numPairs = dim(pData(eset))[1]/2
expressionDataGEO=importExpressionDataGEO(eset,gpl,defaultProbeSelector,probeCombinerMean)
experimentDataGEO=runTestOnData(expressionDataGEO,1:60,61:120,logPairedTTestFunction)

## End(Not run)

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