Man pages for singha53/amritr
Accessory Functions Used by Amrit Singh

annotateTranscriptstable of classification performances
biomarkerPipelinebiomarkerPipeline
calculateDiffcalculate difference between edge scores
CIBERSORTMain functions
colSdscolSds
colVarscolVars
compVartable of classification performances
CoreAlgCIBERSORT R script v1.03 (last updated 07-10-2015) Note:...
createFoldscreateFolds function copied from the caret R-package
customThemecustomeTheme fucntion for ggplot
descriptiveStatCalculate desriptive statistics for each group and compare...
doPermdo permutations
enetElastic net classification panel
enetCVinteral function (enet cross-validation)
ensembleEnetBuild ensemble enet classification panel
ensembleEnetCVEstimate classification performance using cross-validation...
ensembleRfBuild ensemble random forest classification panel
ensembleRfCVEstimate classification performance using cross-validation...
ensemble.splsdaBuild ensemble sPLSDA classification panel
ensemble.splsdaCVEstimate cross-validation error using cross-validation
ensembleSvmtable of classification performances
ensembleSvmCVtable of classification performances
extendedBICcompute BIC value
extractErrclean up diablo perf() output
fast.dingoPerform DINGO
fast.scoring.bootrecompute differential edge scores
gene_set_analysisGene Set Analysis (GSA)
glmCVinteral function (glm cross-validation)
glmPanelGLM single biomarker
graphIndicesgraphIndices()
hypothesisTestsperform hypothesis test based on variable type
integrativePanelsintegrativePanels()
IntersectIntersection function
lme_interactionBinaryConttable of classification performances
lm_singlePredictortable of classification performances
multiplottable of classification performances
networkStatsnetworkStats()
normalizelibSumtable of classification performances
normalizeNetworknormalizeNetwork
pandaModifrun PANDA (calculate geneCoreg, regNet and co-operative...
pandaxCaculate difference between regulatory coefficients of the...
pandaxBootCaculate differential regulatory network statistics
panel.cortable of classification performances
perf.enetcross-validation function for elastic net panel
perf.ensembleEnetEstimate classification performance using repeated...
perf.ensembleRfEstimate classification performance using repeated...
perfEnsemble.splsdaEstimate test error using repeated cross-validation
perfEnsembleSvmtable of classification performances
perf.glmcross-validation function for glm
perf.rfCross-validation repeated iter number of times
perf.sPLSDArepeated CV function for a sPLSDA model
perf.svmcross-validation function for svm panel
perf.tuned.sPLSDARuns a cross-validation scheme a given number (iter) of times
plotSampleHisttable of classification performances
rccToDatConvert .RCC file to data frame
rfCVcross-validation for a random forest panel
rforestRandom forest classification panel
rowSdsrowSds
rowVarsrowVars
setDesignclean up diablo perf() output
SetdiffSetdiff function
splitDatasplit demographics into two datasets (continuous and...
sPLSDAsPLSDA function
sPLSDACVCV function for a sPLSDA model
supportVectorMachineSVM classification panel
svmCVinteral function (svm cross-validation)
tanimototanimoto
tperformancetable of classification performances
tuned.sPLSDAsPLSDA model after tuning of the number of variables
tuned.sPLSDACVRuns a cross-validation scheme for a tuned.splsda model once
UnionUnion function
update.diagonalupdate.diagonal
venndiagramVenn Diagram
vennDualOverlap between 2 sets
vennQuadOverlap between 4 sets
vennTripleOverlap between 3 sets
zip_nPuretable of classification performances
singha53/amritr documentation built on Nov. 19, 2017, 3:38 a.m.