# Summarize, Analyze and Visualize MAF Files

## Documentation for package ‘maftools’ version 2.22.0

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

## Help Pages

annovarToMaf | Converts annovar annotations into MAF.
bamreadcounts | extract nucleotide counts for targeted variants from the BAM file.
cancerhotspots | Genotype known cancer hotspots from the tumor BAM file
cancerhotspotsAggr | Aggregate cancerhotspots reports
clinicalEnrichment | Performs mutational enrichment analysis for a given clinical feature.
coBarplot | Draw two barplots side by side for cohort comparision.
coGisticChromPlot | Co-plot version of gisticChromPlot()
compareSignatures | Compares identified denovo mutational signatures to known COSMIC signatures
coOncoplot | Draw two oncoplots side by side for cohort comparision.
drugInteractions | Drug-Gene Interactions
estimateSignatures | Estimate number of signatures based on cophenetic correlation metric
extractSignatures | Extract mutational signatures from trinucleotide context.
filterMaf | Filter MAF objects
forestPlot | Draw forest plot for differences betweeen cohorts.
genesToBarcodes | Extracts Tumor Sample Barcodes where the given genes are mutated.
genotypeMatrix | Creates a Genotype Matrix for every variant
getClinicalData | extract annotations from MAF object
getClinicalData-method | extract annotations from MAF object
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
gisticBubblePlot | Plot gistic results as a bubble plot
gisticChromPlot | Plot gistic results along linearized chromosome
gisticCompare | compare two GISTIC objects
gisticOncoPlot | Plot gistic results.
gtMarkers | Extract read counts from genetic markers for ASCAT analysis
icgcSimpleMutationToMAF | Converts ICGC Simple Somatic Mutation format file to MAF
inferHeterogeneity | Clusters variants based on Variant Allele Frequencies (VAF).
intersectMAF | Set Operations for MAF objects
lollipopPlot | Draws lollipop plot of amino acid changes on to Protein structure.
lollipopPlot2 | Compare two lollipop plots
MAF | Construct an MAF object
MAF-class | Class MAF
maf2mae | Convert MAF to MultiAssayExperiment object
mafbarplot | Creates a bar plot
mafCompare | compare two cohorts (MAF).
mafSummary | Summary statistics of MAF
mafSurvGroup | Performs survival analysis for a geneset
mafSurvival | Performs survival analysis
math.score | calculates MATH (Mutant-Allele Tumor Heterogeneity) score.
merge_mafs | Merge multiple mafs into single MAF
mutCountMatrix | Generates count matrix of mutations.
oncodrive | Detect cancer driver genes based on positional clustering of variants.
oncoplot | draw an oncoplot
oncostrip | draw an oncostrip similar to cBioportal oncoprinter output.
pathways | Enrichment of known oncogenic or custom pathways
pfamDomains | pfam domain annotation and summarization.
plotApobecDiff | Plot differences between APOBEC enriched and non-APOBEC enriched samples.
plotCBSsegments | Plots segmented copy number data.
plotClusters | Plot density plots from clutering results.
plotCophenetic | Draw an elbow plot of cophenetic correlation metric.
plotEnrichmentResults | Plots results from clinicalEnrichment analysis
plotmafSummary | Plots maf summary.
plotMosdepth | Plot results from mosdepth output for Tumor/Normal pair
plotMosdepth_t | Plot results from mosdepth output
plotOncodrive | Plots results from 'oncodrive'
plotPathways | Plot oncogenic pathways
plotProtein | Display protein domains
plotSignatures | Plots decomposed mutational signatures
plotTiTv | Plot Transition and Trasnversion ratios.
plotVaf | Plots vaf distribution of genes
prepareMutSig | Prepares MAF file for MutSig analysis.
prepAscat | Prepare input files for ASCAT
prepAscat_t | Prepare input files for ASCAT tumor only samples
rainfallPlot | Rainfall plot to display hyper mutated genomic regions.
read.maf | Read MAF files.
readGistic | Read and summarize gistic output.
sampleSwaps | Identify sample swaps and similarities
segmentLogR | Segment and plot log ratio values with DNACopy
segSummarize | Summarize CBS segmentation results
setdiffMAF | Set Operations for MAF objects
signatureEnrichment | Performs sample stratification based on signature contribution and enrichment analysis.
somaticInteractions | Exact tests to detect mutually exclusive, co-occuring and altered genesets.
subsetMaf | Subset MAF objects
survGroup | Predict genesets associated with survival
tcgaAvailable | Prints available TCGA datasets
tcgaCompare | Compare mutation load against TCGA cohorts
tcgaDriverBP | Compare genes to known TCGA drivers and their biological pathways
tcgaLoad | Loads a TCGA cohort
titv | Classifies SNPs into transitions and transversions
tmb | Estimate Tumor Mutation Burden
trinucleotideMatrix | Extract single 5' and 3' bases flanking the mutated site for de-novo signature analysis. Also estimates APOBEC enrichment scores.
vafCompare | compare VAF across two cohorts
write.GisticSummary | Writes GISTIC summaries to output tab-delimited text files.
write.mafSummary | Writes maf summaries to output tab-delimited text files.