API for maftools
Summarize, Analyze and Visualize MAF Files

Global functions
GISTIC Man page
GISTIC-class Man page
MAF Man page
MAF-class Man page
add_oncoprint Source code
add_oncoprint2 Source code
annovarToMaf Man page Source code
cluster_prot Source code
coOncoplot Man page Source code
createOncoMatrix Source code
dashboard Source code
detectCP Source code
dirichletClusters 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 Man page
getClinicalData,MAF-method Man page
getCytobandSummary Man page Man page
getCytobandSummary,GISTIC-method Man page
getFields Man page Man page
getFields,MAF-method Man page
getGeneSummary Man page Man page Man page
getGeneSummary,GISTIC-method Man page
getGeneSummary,MAF-method Man page
getOncoPlot Source code
getSampleSummary Man page Man page Man page
getSampleSummary,GISTIC-method Man page
getSampleSummary,MAF-method Man page
get_threshold 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
lollipopPlot 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
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
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
somaticInteractions Man page Source code
sortByAnnotation Source code
sortByGeneOrder Source code
sortByMutation 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
maftools documentation built on Dec. 14, 2017, 6:22 a.m.