Man pages for PoisonAlien/maftools
Summarize, Analyze and Visualize MAF Files

annovarToMafConverts annovar annotations into MAF.
clinicalEnrichmentPerforms mutational enrichment analysis for a given clinical...
coOncoplotDraw two oncoplots side by side for cohort comparision.
extractSignaturesExtract mutational signatures from trinucleotide context.
forestPlotDraw forest plot for differences betweeen cohorts.
geneCloudPlots wordcloud.
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
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
mafSurvivalPerforms survival analysis
math.scorecalculates MATH (Mutant-Allele Tumor Heterogeneity) score.
mutCountMatrixGenerates count matrix of mutations.
oncodriveDetect cancer driver genes based on positional clustering of...
oncoplotdraw an oncoplot
oncostripdraw an oncostrip similar to cBioportal oncoprinter output.
oncotateAnnotates given variants using oncotator api.
pancanComparisonPerform PacCancer analysis
pfamDomainspfam domain annotation and summarization.
plotApobecDiffPlot differences between APOBEC enriched and non-APOBEC...
plotCBSsegmentsPlots segmented copy number data.
plotClustersPlot density plots from clutering results.
plotEnrichmentResultsPlots results from clinicalEnrichment analysis
plotmafSummaryPlots maf summary.
plotOncodrivePlots results from 'oncodrive'
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.
signatureEnrichmentPerforms sample stratification based on signature...
somaticInteractionsExact tests to detect mutually exclusive, co-occuring and...
subsetMafSubset MAF
tcgaCompareCompare mutation load against TCGA cohorts
titvClassifies SNPs into transitions and transversions
trinucleotideMatrixExtract single 5' and 3' bases flanking the mutated site for...
write.GisticSummaryWrites GISTIC summaries to output tab-delimited text files.
write.mafSummaryWrites maf summaries to output tab-delimited text files.
PoisonAlien/maftools documentation built on April 24, 2018, 9:18 a.m.