computePathwayScores: Compute the pathway scores from the pageRanks.

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

Description

This function computes the pathway scores for the given pathways and the pageRanks using the passed distanceFunction

Usage

computePathwayScores(pageRanks, pathwayMembership, distanceFunction,
  distanceFunctionExtraArgs)

Arguments

pageRanks	A data frame with two columns containing the normal page rank and the disease page rank. There are as many rows as number of HGNC Symbols in PPI Graph. The output from computePageRanks
pathwayMembership	A list containing two elements - pathways- a single column data frame with description string for each unique pathway id memberships - a list of character vectors of gene ids indexed by pathway id, containing the list of hgnc symbols of genes in each pathway. The output of loadPathwayDataReactome
distanceFunction	A function to compare the normal and disease pagerank vectors. See KLDivergenceDistanceFunction or meanAbsoluteDeviationDistanceFunction foe examples
distanceFunctionExtraArgs	A list of extra arguments to be passed to the distance function if any.

Value

A data frame containing the deviation score for each pathway.

Examples

## Not run: 
gds = getGEO('GDS3837',AnnotGPL = TRUE, getGPL = TRUE,destdir =
"/tmp") gpl = getGEO(Meta(gds)$platform,destdir = "/tmp") eset =
GDS2eSet(gds, GPL=gpl,do.log2=FALSE) numPairs = dim(pData(eset))[1]/2
expressionDataGEO=importExpressionDataGEO(eset,gpl,defaultProbeSelector,probeCombinerMean)
experimentDataGEO=runTestOnData(expressionDataGEO,1:60,61:120,logPairedTTestFunction)
personalizationVectorsGEO=computePersonalizationVectors(experimentDataGEO,reactomePPIGraph,data.frame(foldChange=1,pValue=1),outdegreeNormalizedFCOneMinusPScoreFunction)
pageRanksGEO=computePageRanks(personalizationVectorsGEO,reactomePPIGraph,0.7)
pathwayScoresGEO=computePathwayScores(pageRanksGEO,reactomePathwayData$pathwayMembership,meanAbsoluteDeviationDistanceFunction,list())

## End(Not run)

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