Summarize, Analyze and Visualize MAF Files

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Documentation for package ‘maftools’ version 2.25.10

• 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.