Man pages for bhatturam/prius
Affected pathway ranking in differential gene expression analysis

computePageRanksCompute the pageRanks for the genes.
computePathwayScoresCompute the pathway scores from the pageRanks.
computePersonalizationVectorsCompute the personalization vectors based on experimental...
createIGraphObjectCreate graph object from gene interaction list
downloadReactomeInteractionsMITABDownload PPI Reactions from Reactome in MITAB format
downloadReactomePathwaysDownload current Pathway Data from Reactome
foldChangeFunctionSimple fold change test function
getGeneInteractionsFromIRefMITABGet a gene interaction data frame from a iRef ppi mitab data...
getGeneInteractionsFromReactomeMITABGet a gene interaction data frame from a reactome ppi mitab...
getUniProtToHGNCSymbolMappingGet a mapping table between UniProt ID's and HGNC Gene...
importExpressionDataGEOImport expression data and probe mappings from GEO dataset
KLDivergenceDistanceFunctionKL Divergence between two vectors.
loadExperimentDataLoad experiment data
loadPathwayDataReactomeLoad pathway data from Reactome
logPairedTTestFunctionPaired t-test based test function
meanAbsoluteDeviationDistanceFunctionMean Absolute Deviation between two vectors.
outdegreeNormalizedFCOneMinusPScoreFunctionOutdegree normalized fold change and p-value based scoring
outdegreeNormalizedFCScoreFunctionOutdegree normalized fold change based scoring
probeCombinerMeanCombine probes by mean expression value
probeSelectorATSATSelect only _at and _a_at probe sets for analysis
runTestOnDataTest expression data
bhatturam/prius documentation built on May 11, 2017, 11:11 a.m.