annovarToMaf	annovarToMaf
clinicalEnrichment	clinicalEnrichment
coBarplot	coBarplot
compareSignatures	compareSignatures
coOncoplot	coOncoplot
drugInteractions	drugInteractions
estimateSignatures	estimateSignatures
extractSignatures	extractSignatures
forestPlot	forestPlot
genesToBarcodes	genesToBarcodes
genotypeMatrix	genotypeMatrix
getClinicalData	getClinicalData
getClinicalData,MAF-method	getClinicalData
getCytobandSummary	getCytobandSummary
getCytobandSummary,GISTIC-method	getCytobandSummary
getFields	getFields
getFields,MAF-method	getFields
getGeneSummary	getGeneSummary
getGeneSummary,GISTIC-method	getGeneSummary
getGeneSummary,MAF-method	getGeneSummary
getSampleSummary	getSampleSummary
getSampleSummary,GISTIC-method	getSampleSummary
getSampleSummary,MAF-method	getSampleSummary
GISTIC	GISTIC-class
GISTIC-class	GISTIC-class
gisticBubblePlot	gisticBubblePlot
gisticChromPlot	gisticChromPlot
gisticOncoPlot	gisticOncoPlot
icgcSimpleMutationToMAF	icgcSimpleMutationToMAF
inferHeterogeneity	inferHeterogeneity
intersectMAF	setMaf
lollipopPlot	lollipopPlot
lollipopPlot2	lollipopPlot2
MAF	MAF-class
MAF-class	MAF-class
mafCompare	mafCompare
mafSummary	mafSummary
mafSurvGroup	mafSurvGroup
mafSurvival	mafSurvival
math.score	math.score
merge_mafs	merge_mafs
mutCountMatrix	mutCountMatrix
oncodrive	oncodrive
OncogenicPathways	OncogenicPathways
oncoplot	oncoplot
oncostrip	oncostrip
pfamDomains	pfamDomains
plotApobecDiff	plotApobecDiff
plotCBSsegments	plotCBSsegments
plotClusters	plotClusters
plotCophenetic	plotCophenetic
plotEnrichmentResults	plotEnrichmentResults
plotmafSummary	plotmafSummary
plotOncodrive	plotOncodrive
PlotOncogenicPathways	PlotOncogenicPathways
plotSignatures	plotSignatures
plotTiTv	plotTiTv
plotVaf	plotVaf
prepareMutSig	prepareMutSig
rainfallPlot	rainfallPlot
read.maf	read.maf
readGistic	readGistic
setdiffMAF	setMaf
signatureEnrichment	signatureEnrichment
somaticInteractions	somaticInteractions
subsetMaf	subsetMaf
survGroup	survGroup
tcgaCompare	tcgaCompare
tcgaDriverBP	tcgaDriverBP
titv	titv
tmb	tmb
trinucleotideMatrix	trinucleotideMatrix
vafCompare	vafCompare
write.GisticSummary	write.GisticSummary
write.mafSummary	write.mafSummary
