Man pages for bhatturam/prius
Affected pathway ranking in differential gene expression analysis
| computePageRanks | Compute the pageRanks for the genes. |
| computePathwayScores | Compute the pathway scores from the pageRanks. |
| computePersonalizationVectors | Compute the personalization vectors based on experimental... |
| createIGraphObject | Create graph object from gene interaction list |
| downloadReactomeInteractionsMITAB | Download PPI Reactions from Reactome in MITAB format |
| downloadReactomePathways | Download current Pathway Data from Reactome |
| foldChangeFunction | Simple fold change test function |
| getGeneInteractionsFromIRefMITAB | Get a gene interaction data frame from a iRef ppi mitab data... |
| getGeneInteractionsFromReactomeMITAB | Get a gene interaction data frame from a reactome ppi mitab... |
| getUniProtToHGNCSymbolMapping | Get a mapping table between UniProt ID's and HGNC Gene... |
| importExpressionDataGEO | Import expression data and probe mappings from GEO dataset |
| KLDivergenceDistanceFunction | KL Divergence between two vectors. |
| loadExperimentData | Load experiment data |
| loadPathwayDataReactome | Load pathway data from Reactome |
| logPairedTTestFunction | Paired t-test based test function |
| meanAbsoluteDeviationDistanceFunction | Mean Absolute Deviation between two vectors. |
| outdegreeNormalizedFCOneMinusPScoreFunction | Outdegree normalized fold change and p-value based scoring |
| outdegreeNormalizedFCScoreFunction | Outdegree normalized fold change based scoring |
| probeCombinerMean | Combine probes by mean expression value |
| probeSelectorATSAT | Select only _at and _a_at probe sets for analysis |
| runTestOnData | Test expression data |
