# Summarize, Analyze and Visualize MAF files

## Documentation for package ‘maftools’ version 1.0.55

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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).
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.
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.
plotmafSummary | Plots maf summary.
plotOncodrive | Plots results from 'oncodrive'
plotSignatures | Plots decomposed mutational signatures.
plotTiTv | Plot Transition and Trasnversion ratios.
plotVaf | Plots vaf distribution of genes
rainfallPlot | Rainfall plot to display kataegis or hyper mutated genomic regions.
read.maf | Read MAF files.
readGistic | Read and summarize gistic output.
subsetMaf | Subset MAF
titv | Classifies SNPs into transitions and transversions
trinucleotideMatrix | Extract single 5' and 3' bases flanking the mutated site.
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.