API for PoisonAlien/maftools
Summarize, Analyze and Visualize MAF Files

Global functions
GISTIC	Man page
GISTIC-class	Man page
MAF	Man page
MAF-class	Man page
OncogenicPathways	Man page Source code
PlotOncogenicPathways	Man page Source code
add_legend	Source code
add_oncoprint	Source code
add_oncoprint2	Source code
annovarToMaf	Man page Source code
binconf	Source code
clinicalEnrichment	Man page Source code
cluster_prot	Source code
coOncoplot	Man page Source code
createOncoMatrix	Source code
dashboard	Source code
detect_kataegis	Source code
detect_kataegis_chr	Source code
dirichletClusters	Source code
drugInteractions	Man page Source code
estimate_binconf	Source code
extractSignatures	Man page Source code
filterCopyNumber	Source code
fisherCorrection	Source code
forestPlot	Man page Source code
geneCloud	Man page Source code
genesToBarcodes	Man page Source code
genotypeMatrix	Man page Source code
getClinicalData	Man page
getClinicalData,MAF-method	Man page
getCytobandSummary	Man page
getCytobandSummary,GISTIC-method	Man page
getFields	Man page
getFields,MAF-method	Man page
getGeneSummary	Man page
getGeneSummary,GISTIC-method	Man page
getGeneSummary,MAF-method	Man page
getOncoPlot	Source code
getSampleSummary	Man page
getSampleSummary,GISTIC-method	Man page
getSampleSummary,MAF-method	Man page
get_lp_data	Source code
get_threshold	Source code
get_titvCol	Source code
get_vcColors	Source code
gisticBubblePlot	Man page Source code
gisticChromPlot	Man page Source code
gisticMap	Source code
gisticOncoPlot	Man page Source code
icgcSimpleMutationToMAF	Man page Source code
inferHeterogeneity	Man page Source code
label_pos	Source code
lollipopPlot	Man page Source code
lollipopPlot2	Man page Source code
mafCompare	Man page Source code
mafSummary	Man page Source code
mafSurvival	Man page Source code
mapMutsToSegs	Source code
math.score	Man page Source code
merge_mafs	Man page Source code
mutCountMatrix	Man page Source code
oncodrive	Man page Source code
oncoplot	Man page Source code
oncostrip	Man page Source code
oncotate	Man page Source code
pancanComparison	Man page Source code
parse_prot	Source code
pfamDomains	Man page Source code
plotApobecDiff	Man page Source code
plotCBS	Source code
plotCBSchr	Source code
plotCBSsegments	Man page Source code
plotClusters	Man page Source code
plotEnrichmentResults	Man page Source code
plotOncodrive	Man page Source code
plotSignatures	Man page Source code
plotTiTv	Man page Source code
plotVaf	Man page Source code
plotmafSummary	Man page Source code
prepareMutSig	Man page Source code
rainfallPlot	Man page Source code
read.maf	Man page Source code
readGistic	Man page Source code
readSegs	Source code
refineClusters	Source code
repelPoints	Source code
shiftPoints	Source code
signatureEnrichment	Man page Source code
somaticInteractions	Man page Source code
sortByAnnotation	Source code
sortByGeneOrder	Source code
sortByMutation	Source code
sortByMutationKeepGeneOrder	Source code
subsetMaf	Man page Source code
summarizeGistic	Source code
summarizeMaf	Source code
tcgaCompare	Man page Source code
titv	Man page Source code
transformSegments	Source code
trinucleotideMatrix	Man page Source code
validateMaf	Source code
write.GisticSummary	Man page Source code
write.mafSummary	Man page Source code