NAMESPACE

# Generated by roxygen2: do not edit by hand

export(MAF)
export(annovarToMaf)
export(bamreadcounts)
export(cancerhotspots)
export(cancerhotspotsAggr)
export(clinicalEnrichment)
export(coBarplot)
export(coGisticChromPlot)
export(coOncoplot)
export(compareSignatures)
export(drugInteractions)
export(estimateSignatures)
export(extractSignatures)
export(filterMaf)
export(forestPlot)
export(genesToBarcodes)
export(genotypeMatrix)
export(gisticBubblePlot)
export(gisticChromPlot)
export(gisticCompare)
export(gisticOncoPlot)
export(gtMarkers)
export(icgcSimpleMutationToMAF)
export(inferHeterogeneity)
export(intersectMAF)
export(lollipopPlot)
export(lollipopPlot2)
export(maf2mae)
export(mafCompare)
export(mafSummary)
export(mafSurvGroup)
export(mafSurvival)
export(mafbarplot)
export(math.score)
export(merge_mafs)
export(mutCountMatrix)
export(oncodrive)
export(oncoplot)
export(oncostrip)
export(pathways)
export(pfamDomains)
export(plotApobecDiff)
export(plotCBSsegments)
export(plotClusters)
export(plotCophenetic)
export(plotEnrichmentResults)
export(plotMosdepth)
export(plotMosdepth_t)
export(plotOncodrive)
export(plotPathways)
export(plotProtein)
export(plotSignatures)
export(plotTiTv)
export(plotVaf)
export(plotmafSummary)
export(prepAscat)
export(prepAscat_t)
export(prepareMutSig)
export(rainfallPlot)
export(read.maf)
export(readGistic)
export(sampleSwaps)
export(segSummarize)
export(segmentLogR)
export(setdiffMAF)
export(signatureEnrichment)
export(somaticInteractions)
export(subsetMaf)
export(survGroup)
export(tcgaAvailable)
export(tcgaCompare)
export(tcgaLoad)
export(titv)
export(tmb)
export(trinucleotideMatrix)
export(vafCompare)
export(write.GisticSummary)
export(write.mafSummary)
exportClasses(GISTIC)
exportClasses(MAF)
exportMethods(getClinicalData)
exportMethods(getCytobandSummary)
exportMethods(getFields)
exportMethods(getGeneSummary)
exportMethods(getSampleSummary)
import(DNAcopy)
import(RColorBrewer)
import(data.table)
import(methods)
import(survival)
importFrom(grDevices,boxplot.stats)
importFrom(grDevices,colors)
importFrom(grDevices,colours)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
useDynLib(maftools, .registration = TRUE)