annovarToMaf	annovarToMaf
coOncoplot	coOncoplot
extractSignatures	extractSignatures
forestPlot	forestPlot
geneCloud	geneCloud
genesToBarcodes	genesToBarcodes
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
gisticPlot	gisticPlot
icgcSimpleMutationToMAF	icgcSimpleMutationToMAF
inferHeterogeneity	inferHeterogeneity
lollipopPlot	lollipopPlot
MAF	MAF-class
MAF-class	MAF-class
mafCompare	mafCompare
math.score	math.score
mutExclusive	mutExclusive
oncodrive	oncodrive
oncoplot	oncoplot
oncostrip	oncostrip
oncotate	oncotate
pfamDomains	pfamDomains
plotCBSsegments	plotCBSsegments
plotClusters	plotClusters
plotGisticResults	plotGisticResults
plotmafSummary	plotmafSummary
plotOncodrive	plotOncodrive
plotSignatures	plotSignatures
plotTiTv	plotTiTv
plotVaf	plotVaf
rainfallPlot	rainfallPlot
read.maf	read.maf
readGistic	readGistic
subsetMaf	subsetMaf
titv	titv
trinucleotideMatrix	trinucleotideMatrix
vcr	vcr
write.GisticSummary	write.GisticSummary
write.mafSummary	write.mafSummary
