Summarize, Analyze and Visualize MAF Files


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Documentation for package ‘maftools’ version 1.2.30

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annovarToMaf Converts annovar annotations into MAF.
coOncoplot Draw two oncoplots side by side for cohort comparision.
extractSignatures Extract mutational signatures from trinucletide context.
forestPlot Draw forest plot for differences betweeen cohorts.
geneCloud Plots wordcloud.
genesToBarcodes Extracts Tumor Sample Barcodes where the given genes are mutated.
getCytobandSummary extract cytoband summary from GISTIC object
getCytobandSummary-method extract cytoband summary from GISTIC object
getFields extract available fields from MAF object
getFields-method extract available fields from MAF object
getGeneSummary extract gene summary from MAF or GISTIC object
getGeneSummary-method extract gene summary from MAF or GISTIC object
getSampleSummary extract sample summary from MAF or GISTIC object
getSampleSummary-method extract sample summary from MAF or GISTIC object
GISTIC Class GISTIC
GISTIC-class Class GISTIC
gisticPlot Plot gistic results.
icgcSimpleMutationToMAF Converts ICGC Simple Somatic Mutation format file to MAF
inferHeterogeneity Clusters variants based on Variant Allele Frequencies (VAF).
lollipopPlot Draws lollipop plot of amino acid changes on to Protein structure.
MAF Class MAF
MAF-class Class MAF
mafCompare compare two cohorts (MAF).
mafSurvival Performs survival analysis
math.score calculates MATH (Mutant-Allele Tumor Heterogeneity) score.
mutExclusive Performs exact test for mutual exclusive events.
oncodrive Detect cancer driver genes based on positional clustering of variants.
oncoplot draw an oncoplot
oncostrip draw an oncostrip similar to cBioportal oncoprinter output.
oncotate Annotates given variants using oncotator api.
pancanComparision Perform PacCancer analysis
pfamDomains pfam domain annotation and summarization.
plotCBSsegments Plots segmented copy number data.
plotClusters Plot density plots from clutering results.
plotGisticResults Plot gistic results as a bubble plot or as a genomic segment plot.
plotmafSummary Plots maf summary.
plotOncodrive Plots results from 'oncodrive'
plotSignatures Plots decomposed mutational signatures or APOBEC enrichment plot.
plotTiTv Plot Transition and Trasnversion ratios.
plotVaf Plots vaf distribution of genes
prepareMutSig Prepares MAF file for MutSig analysis.
rainfallPlot Rainfall plot to display hyper mutated genomic regions.
read.maf Read MAF files.
readGistic Read and summarize gistic output.
subsetMaf Subset MAF
tcgaCompare Compare mutation load against TCGA cohorts
titv Classifies SNPs into transitions and transversions
trinucleotideMatrix Extract single 5' and 3' bases flanking the mutated site for de-novo signature analysis. Also estimates APOBEC enrichment scores.
vcr Samll internal function to make complex events.
write.GisticSummary Writes GISTIC summaries to output tab-delimited text files.
write.mafSummary Writes maf summaries to output tab-delimited text files.