Man pages for singha53/amritr
Accessory Functions Used by Amrit Singh
| annotateTranscripts | table of classification performances |
| biomarkerPipeline | biomarkerPipeline |
| calculateDiff | calculate difference between edge scores |
| CIBERSORT | Main functions |
| colSds | colSds |
| colVars | colVars |
| compVar | table of classification performances |
| CoreAlg | CIBERSORT R script v1.03 (last updated 07-10-2015) Note:... |
| createFolds | createFolds function copied from the caret R-package |
| customTheme | customeTheme fucntion for ggplot |
| descriptiveStat | Calculate desriptive statistics for each group and compare... |
| doPerm | do permutations |
| enet | Elastic net classification panel |
| enetCV | interal function (enet cross-validation) |
| ensembleEnet | Build ensemble enet classification panel |
| ensembleEnetCV | Estimate classification performance using cross-validation... |
| ensembleRf | Build ensemble random forest classification panel |
| ensembleRfCV | Estimate classification performance using cross-validation... |
| ensemble.splsda | Build ensemble sPLSDA classification panel |
| ensemble.splsdaCV | Estimate cross-validation error using cross-validation |
| ensembleSvm | table of classification performances |
| ensembleSvmCV | table of classification performances |
| extendedBIC | compute BIC value |
| extractErr | clean up diablo perf() output |
| fast.dingo | Perform DINGO |
| fast.scoring.boot | recompute differential edge scores |
| gene_set_analysis | Gene Set Analysis (GSA) |
| glmCV | interal function (glm cross-validation) |
| glmPanel | GLM single biomarker |
| graphIndices | graphIndices() |
| hypothesisTests | perform hypothesis test based on variable type |
| integrativePanels | integrativePanels() |
| Intersect | Intersection function |
| lme_interactionBinaryCont | table of classification performances |
| lm_singlePredictor | table of classification performances |
| multiplot | table of classification performances |
| networkStats | networkStats() |
| normalizelibSum | table of classification performances |
| normalizeNetwork | normalizeNetwork |
| pandaModif | run PANDA (calculate geneCoreg, regNet and co-operative... |
| pandax | Caculate difference between regulatory coefficients of the... |
| pandaxBoot | Caculate differential regulatory network statistics |
| panel.cor | table of classification performances |
| perf.enet | cross-validation function for elastic net panel |
| perf.ensembleEnet | Estimate classification performance using repeated... |
| perf.ensembleRf | Estimate classification performance using repeated... |
| perfEnsemble.splsda | Estimate test error using repeated cross-validation |
| perfEnsembleSvm | table of classification performances |
| perf.glm | cross-validation function for glm |
| perf.rf | Cross-validation repeated iter number of times |
| perf.sPLSDA | repeated CV function for a sPLSDA model |
| perf.svm | cross-validation function for svm panel |
| perf.tuned.sPLSDA | Runs a cross-validation scheme a given number (iter) of times |
| plotSampleHist | table of classification performances |
| rccToDat | Convert .RCC file to data frame |
| rfCV | cross-validation for a random forest panel |
| rforest | Random forest classification panel |
| rowSds | rowSds |
| rowVars | rowVars |
| setDesign | clean up diablo perf() output |
| Setdiff | Setdiff function |
| splitData | split demographics into two datasets (continuous and... |
| sPLSDA | sPLSDA function |
| sPLSDACV | CV function for a sPLSDA model |
| supportVectorMachine | SVM classification panel |
| svmCV | interal function (svm cross-validation) |
| tanimoto | tanimoto |
| tperformance | table of classification performances |
| tuned.sPLSDA | sPLSDA model after tuning of the number of variables |
| tuned.sPLSDACV | Runs a cross-validation scheme for a tuned.splsda model once |
| Union | Union function |
| update.diagonal | update.diagonal |
| venndiagram | Venn Diagram |
| vennDual | Overlap between 2 sets |
| vennQuad | Overlap between 4 sets |
| vennTriple | Overlap between 3 sets |
| zip_nPure | table of classification performances |
