Man pages for maftools
Summarize, Analyze and Visualize MAF Files

annovarToMafConverts annovar annotations into MAF.
clinicalEnrichmentPerforms mutational enrichment analysis for a given clinical...
coBarplotDraw two barplots side by side for cohort comparision.
compareSignaturesCompares identified denovo mutational signatures to known...
coOncoplotDraw two oncoplots side by side for cohort comparision.
drugInteractionsDrug-Gene Interactions
estimateSignaturesEstimate number of signatures based on cophenetic correlation...
extractSignaturesExtract mutational signatures from trinucleotide context.
filterMafFilter MAF objects
forestPlotDraw forest plot for differences betweeen cohorts.
genesToBarcodesExtracts Tumor Sample Barcodes where the given genes are...
genotypeMatrixCreates a Genotype Matrix for every variant
getClinicalDataextract annotations from MAF object
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
gisticBubblePlotPlot gistic results as a bubble plot
gisticChromPlotPlot gistic results along linearized chromosome
GISTIC-classClass GISTIC
gisticOncoPlotPlot 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...
lollipopPlot2Compare two lollipop plots
MAF-classClass MAF
mafComparecompare two cohorts (MAF).
mafSummarySummary statistics of MAF
mafSurvGroupPerforms survival analysis for a geneset
mafSurvivalPerforms survival analysis
math.scorecalculates MATH (Mutant-Allele Tumor Heterogeneity) score.
merge_mafsMerge multiple mafs into single MAF
mutCountMatrixGenerates count matrix of mutations.
oncodriveDetect cancer driver genes based on positional clustering of...
OncogenicPathwaysEnrichment of known oncogenic pathways
oncoplotdraw an oncoplot
oncostripdraw an oncostrip similar to cBioportal oncoprinter output.
pfamDomainspfam domain annotation and summarization.
plotApobecDiffPlot differences between APOBEC enriched and non-APOBEC...
plotCBSsegmentsPlots segmented copy number data.
plotClustersPlot density plots from clutering results.
plotCopheneticDraw an elbow plot of cophenetic correlation metric.
plotEnrichmentResultsPlots results from clinicalEnrichment analysis
plotmafSummaryPlots maf summary.
plotOncodrivePlots results from 'oncodrive'
PlotOncogenicPathwaysPlot oncogenic pathways
plotSignaturesPlots decomposed mutational signatures
plotTiTvPlot Transition and Trasnversion ratios.
plotVafPlots vaf distribution of genes
prepareMutSigPrepares MAF file for MutSig analysis.
rainfallPlotRainfall plot to display hyper mutated genomic regions.
readGisticRead and summarize gistic output.
read.mafRead MAF files.
setMafSet Operations for MAF objects
signatureEnrichmentPerforms sample stratification based on signature...
somaticInteractionsExact tests to detect mutually exclusive, co-occuring and...
subsetMafSubset MAF objects
survGroupPredict genesets associated with survival
tcgaCompareCompare mutation load against TCGA cohorts
tcgaDriverBPCompare genes to known TCGA drivers and their biological...
titvClassifies SNPs into transitions and transversions
tmbEstimate Tumor Mutation Burden
trinucleotideMatrixExtract single 5' and 3' bases flanking the mutated site for...
vafComparecompare VAF across two cohorts
write.GisticSummaryWrites GISTIC summaries to output tab-delimited text files.
write.mafSummaryWrites maf summaries to output tab-delimited text files.
maftools documentation built on Feb. 6, 2021, 2 a.m.