Man pages for BIMIB-DISCo/TRONCO
TRONCO, an R package for TRanslational ONCOlogy

aCMLAtypical chronic myeloid leukemia dataset
ANDAND
annotate.descriptionannotate.description
annotate.stagesannotate.stages
as.adj.matrixas.adj.matrix
as.alterationsas.alterations
as.bootstrap.scoresas.bootstrap.scores
as.colorsas.colors
as.conditional.probsas.conditional.probs
as.confidenceas.confidence
as.descriptionas.description
as.eventsas.events
as.events.in.patternsas.events.in.patterns
as.events.in.sampleas.events.in.sample
as.geneas.gene
as.genesas.genes
as.genes.in.patternsas.genes.in.patterns
as.genotypesas.genotypes
as.hypothesesas.hypotheses
as.joint.probsas.joint.probs
as.kfold.elossas.kfold.eloss
as.kfold.posterras.kfold.posterr
as.kfold.prederras.kfold.prederr
as.marginal.probsas.marginal.probs
as.modelsas.models
as.parametersas.parameters
as.pathwayas.pathway
as.patternsas.patterns
as.samplesas.samples
as.selective.advantage.relationsas.selective.advantage.relations
as.stagesas.stages
as.typesas.types
as.types.in.patternsas.types.in.patterns
cbio.querycbio.query
change.colorchange.color
consolidate.dataconsolidate.data
crc_gisticGISTIC example data
crc_mafMAF example data
crc_plainPlain mutation dataset
delete.eventdelete.event
delete.genedelete.gene
delete.hypothesisdelete.hypothesis
delete.modeldelete.model
delete.patterndelete.pattern
delete.samplesdelete.samples
delete.typedelete.type
duplicatesduplicates
ebindebind
enforce.numericenforce.numeric
enforce.stringenforce.string
events.selectionevents.selection
export.graphmlexport.graphml
export.mutexexport,mutex
export.nbs.inputexport.nbs.input
extract.MAF.HuGO.Entrez.mapextract.MAF.HuGO.Entrez.map
genes.table.reportgenes.table.report
has.duplicateshas.duplicates
has.modelhas.model
has.stageshas stages
hypothesis.addhypothesis add
hypothesis.add.grouphypothesis add group
hypothesis.add.homologoushypothesis.add.homologous
import.genotypesimport.genotypes
import.GISTICimport.GISTIC
import.MAFimport.MAF
import.mutex.groupsimport.mutex.groups
intersect.datasetsintersect.datasets
is.compliantis.compliant
join.eventsjoin.events
join.typesjoin.types
keysToNameskeysToNames
mafMAF example data
mutsSimple mutation dataset
nameToKeynameToKey
neventsnevents
ngenesngenes
nhypothesesReturn the number of hypotheses in the dataset
npatternsReturn the number of patterns in the dataset
nsamplesnsamples
ntypesntypes
oncoprintoncoprint
oncoprint.cbiooncoprint.cbio
OROR
order.frequencyorder.frequency
pathway.visualizationpathway.visualization
pheatmapA function to draw clustered heatmaps.
rank.recurrentsrank.recurrents
rename.generename.gene
rename.typerename.type
samples.selectionsamples.selection
sbindsbind
ssplitssplit
stageStage information for test_dataset
TCGA.map.clinical.dataTCGA.map.clinical.data
TCGA.multiple.samplesTCGA.multiple.samples
TCGA.remove.multiple.samplesTCGA.remove.multiple.samples
TCGA.shorten.barcodesTCGA.shorten.barcodes
test_datasetA complete dataset with hypotheses
test_dataset_no_hyposA complete dataset
test_modelA complete dataset with a reconstructed model
test_model_kfoldA complete dataset with a reconstructed model and...
trimtrim
tronco.bootstraptronco bootstrap
tronco.capresetronco caprese
tronco.capritronco capri
tronco.chowliuTronco Chow Liu
tronco.edmondsTronco Edmonds
tronco.gabowTronco Gabow
tronco.kfold.elosstronco.kfold.eloss
tronco.kfold.posterrtronco.kfold.posterr. For details and examples regarding the...
tronco.kfold.prederrtronco.kfold.prederr
tronco.pattern.plottronco.pattern.plot
tronco.plottronco.plot
tronco.primTronco Prim
viewview
which.sampleswhich.samples
XORXOR
BIMIB-DISCo/TRONCO documentation built on Sept. 17, 2017, 4:59 p.m.