Man pages for cavei/houseOfClipUtility
Clip Legacy Functions
| averageReplicateMatrices | Average a list of Matrices (cell wise) |
| computeFreqs | Compute frequences from list |
| computePCs | Topological PCA |
| computePCsWithResampling | Compute PCs. |
| computeSimPATHyParameters | Compute SimPATHy Parameters |
| convertIds | Ids converter |
| createSignificanceMask | Create a significance matrix |
| downloadPathwayRelationFromReactome | Download Reactome Pathway Relations |
| estimateCov | Estimate Covariance |
| estimateExprCov | Estimate Single Covariance Matrix |
| filterDirected | Filter direct edges |
| getPathFathers | Retrieves pathways relatives |
| graph-processing | Extract the maximal cliques |
| id2name | Convert id to pathway name |
| makeDegreesEven | Forse random nodes degress to be even |
| makePositiveDefinite | Make positive and definite covariance matrix |
| mapFromDict | Map ids using a dict. |
| mapPathwaysIDfromGraphite | Map Pathways ID from Graphite |
| mergeGraphitePathways | Merge graphite Pathways |
| minOrNA | Minimum or NA |
| plotFrequencies | Plot frequences |
| plotPathInGraphNEL | Plot graphNEL with some nodes boerde highlighted |
| randomExpression | Create fake expression based on variance |
| ReactomePathwaysRelation | This is a copy of the file... |
| removeSelfLoops | Remove self loops from a graphNEL |
| reverseDict | Invert The Dictionary |
| simulateData | Simulate Survival Data |
| simulate_expression_dataset | Simulate an expression dataset from survival annotation |
| simulate_methylation_dataset | Simulate a methylation dataset with survival annotation |
| simulate_mutation_dataset | Simulate a mutation dataset with survival annotation |
| subPathway | Subset of a graphite Pathway |
| summarizeOmicsResByMinPvalue | Summarize Omics Covaraites By Min Pvalue |
