Man pages for Bioconductor-mirror/maftools
Summarize, Analyze and Visualize MAF Files

annovarToMafConverts annovar annotations into MAF.
coOncoplotDraw two oncoplots side by side for cohort comparision.
extractSignaturesExtract mutational signatures from trinucletide context.
forestPlotDraw forest plot for differences betweeen cohorts.
geneCloudPlots wordcloud.
genesToBarcodesExtracts Tumor Sample Barcodes where the given genes are...
getCytobandSummaryextract cytoband summary from GISTIC object
getFieldsextract available fields from MAF object
getGeneSummaryextract gene summary from MAF or GISTIC object
getSampleSummaryextract sample summary from MAF or GISTIC object
GISTIC-classClass GISTIC
gisticPlotPlot gistic results.
icgcSimpleMutationToMAFConverts ICGC Simple Somatic Mutation format file to MAF
inferHeterogeneityClusters variants based on Variant Allele Frequencies (VAF).
lollipopPlotDraws lollipop plot of amino acid changes on to Protein...
MAF-classClass MAF
mafComparecompare two cohorts (MAF).
mafSurvivalPerforms survival analysis
math.scorecalculates MATH (Mutant-Allele Tumor Heterogeneity) score.
mutExclusivePerforms exact test for mutual exclusive events.
oncodriveDetect cancer driver genes based on positional clustering of...
oncoplotdraw an oncoplot
oncostripdraw an oncostrip similar to cBioportal oncoprinter output.
oncotateAnnotates given variants using oncotator api.
pancanComparisionPerform PacCancer analysis
pfamDomainspfam domain annotation and summarization.
plotCBSsegmentsPlots segmented copy number data.
plotClustersPlot density plots from clutering results.
plotGisticResultsPlot gistic results as a bubble plot.
plotmafSummaryPlots maf summary.
plotOncodrivePlots results from 'oncodrive'
plotSignaturesPlots decomposed mutational signatures.
plotTiTvPlot Transition and Trasnversion ratios.
plotVafPlots vaf distribution of genes
prepareMutSigPrepares MAF file for MutSig analysis.
rainfallPlotRainfall plot to display kataegis or hyper mutated genomic...
readGisticRead and summarize gistic output.
read.mafRead MAF files.
subsetMafSubset MAF
tcgaCompareCompare mutation load against TCGA cohorts
titvClassifies SNPs into transitions and transversions
trinucleotideMatrixExtract single 5' and 3' bases flanking the mutated site.
vcrSamll internal function to make complex events.
write.GisticSummaryWrites GISTIC summaries to output tab-delimited text files.
write.mafSummaryWrites maf summaries to output tab-delimited text files.
Bioconductor-mirror/maftools documentation built on June 1, 2017, 11:43 a.m.