computePersonalizationVectors: Compute the personalization vectors based on experimental...

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

Description

This function computes the personalization vectors from the experiment data based on an input score function based on the test parameters.

Usage

computePersonalizationVectors(experimentalData, PPIGraph, defaults,
  scoreFunction, scoreFunctionExtraArgs)

Arguments

experimentalData	experimentalData A data frame with as many rows as HGNC Gene Symbols, with the columns defined by the output of testFunction. The output of runTestOnData.
PPIGraph	PPIGraph A list containing igraph_object - the igraph object and vertex_map - a frame containing node attributes currently indegree and outdegree. The output of createIGraphObject
defaults	A data frame corresspoding to the default experimental values for genes missing from the experiment. This must be of the same format as the output of the scoreFunction.
scoreFunction	A score function that accepts the experimentalData and the PPI Graph to return the normal and disease personalization vectors. Foe example see outdegreeNormalizedFCScoreFunction or outdegreeNormalizedFCOneMinusPScoreFunction
scoreFunctionExtraArgs	A list of extra arguments that are to be passed to the score function if any.

Value

A data frame with two columns npv - normal personalization vector and dpv - disease personalization vector. There are as many rows as number of HGNC Symbols in PPIGraph

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)

## End(Not run)

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