maftools: Summarize, Analyze and Visualize MAF Files
Version 1.2.30

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

Browse man pages Browse package API and functions Browse package files

AuthorAnand Mayakonda <anand_mt@hotmail.com>
Bioconductor views Classification DNASeq DataRepresentation DriverMutation FeatureExtraction FunctionalGenomics Sequencing SomaticMutation VariantAnnotation Visualization
Date of publicationNone
MaintainerAnand Mayakonda <anand_mt@hotmail.com>
LicenseMIT + file LICENSE
Version1.2.30
URL https://github.com/PoisonAlien/maftools
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("maftools")

Man 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...
getCytobandSummary: extract cytoband summary from GISTIC object
getFields: extract available fields from MAF object
getGeneSummary: extract gene summary from MAF or GISTIC object
getSampleSummary: extract sample summary from MAF or GISTIC object
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...
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...
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...
plotmafSummary: Plots maf summary.
plotOncodrive: Plots results from 'oncodrive'
plotSignatures: Plots decomposed mutational signatures or APOBEC enrichment...
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.
readGistic: Read and summarize gistic output.
read.maf: Read MAF files.
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...
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.

Functions

GISTIC Man page
GISTIC-class Man page
MAF Man page
MAF-class Man page
add_oncoprint Source code
add_oncoprint2 Source code
annovarToMaf Man page Source code
cluster_prot Source code
coOncoplot Man page Source code
createOncoMatrix Source code
dashboard Source code
dirichletClusters Source code
extractSignatures Man page Source code
filterCopyNumber Source code
fisherCorrection Source code
forestPlot Man page Source code
geneCloud Man page Source code
genesToBarcodes Man page Source code
getCytobandSummary Man page Man page
getCytobandSummary,GISTIC-method Man page
getFields Man page Man page
getFields,MAF-method Man page
getGeneSummary Man page Man page Man page
getGeneSummary,GISTIC-method Man page
getGeneSummary,MAF-method Man page
getOncoPlot Source code
getSampleSummary Man page Man page Man page
getSampleSummary,GISTIC-method Man page
getSampleSummary,MAF-method Man page
get_threshold Source code
gisticMap Source code
gisticPlot Man page Source code
icgcSimpleMutationToMAF Man page Source code
inferHeterogeneity Man page Source code
lollipopPlot Man page Source code
mafCompare Man page Source code
mafSurvival Man page Source code
mapMutsToSegs Source code
math.score Man page Source code
mutExclusive Man page Source code
oncodrive Man page Source code
oncoplot Man page Source code
oncostrip Man page Source code
oncotate Man page Source code
pancanComparision Man page Source code
parse_prot Source code
pfamDomains Man page Source code
plotCBS Source code
plotCBSchr Source code
plotCBSsegments Man page Source code
plotClusters Man page Source code
plotGisticResults Man page Source code
plotOncodrive Man page Source code
plotSignatures Man page Source code
plotTiTv Man page Source code
plotVaf Man page Source code
plotmafSummary Man page Source code
prepareMutSig Man page Source code
rainfallPlot Man page Source code
read.maf Man page Source code
readGistic Man page Source code
readSegs Source code
refineClusters Source code
repelPoints Source code
shiftPoints Source code
sortByAnnotation Source code
sortByMutation Source code
subsetMaf Man page Source code
summarizeGistic Source code
summarizeMaf Source code
tcgaCompare Man page Source code
titv Man page Source code
transformSegments Source code
trinucleotideMatrix Man page Source code
validateMaf Source code
vcr Man page Source code
write.GisticSummary Man page Source code
write.mafSummary Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/TrinucleotideMatrix.R
R/addOncoprint.R
R/annovarToMaf.R
R/clusterScore.R
R/coOncoplot.R
R/dashboard.R
R/domainSummary.R
R/extractSignatures.R
R/filterCopyNumber.R
R/fisherCorrect.R
R/forestPlot.R
R/geneCloud.R
R/genesToBarcodes.R
R/getOncoPlot.R
R/gisticObject.R
R/gisticPlot.R
R/icgc_to_maf.R
R/inferTumHetero.R
R/lollipopPlot.R
R/mafCompare.R
R/mafObjects.R
R/mafSuvival.R
R/maf_methods.R
R/mathScore.R
R/mutExclusive.R
R/oncodrive.R
R/oncoplot.R
R/oncostrip.R
R/oncotate.R
R/pancanAnalysis.R
R/plotClusters.R
R/plotGisticResults.R
R/plotMafSummary.R
R/plotOncodriveClust.R
R/plotSignatures.R
R/plotTiTv.R
R/plot_cbs_segs.R
R/plot_vaf.R
R/prepareMutSig.R
R/rainfallPlot.R
R/readGistic.R
R/readSegs.R
R/read_maf_dt.R
R/refineClusters.R
R/repelPoints.R
R/subsetMaf.R
R/summarizeGistic.R
R/summarizeMaf.R
R/tcgacompare.R
R/titv.R
R/validateMaf.R
R/vcr.R
R/writeGisticSummary.R
R/wrteMafSummary.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/maftools.R
inst/doc/maftools.Rmd
inst/doc/maftools.html
inst/extdata
inst/extdata/APL_primary.maf.gz
inst/extdata/APL_relapse.maf.gz
inst/extdata/LAML_sig_genes.txt.gz
inst/extdata/TCGA.AB.3009.hg19.seg.txt
inst/extdata/all_lesions.conf_99.txt
inst/extdata/amp_genes.conf_99.txt
inst/extdata/coad.maf.gz
inst/extdata/del_genes.conf_99.txt
inst/extdata/ensGenes.txt.gz
inst/extdata/hugo_to_mutSigSymbol.txt.gz
inst/extdata/laml_survival.tsv
inst/extdata/pancan.txt.gz
inst/extdata/prot_len.txt.gz
inst/extdata/protein_domains.txt.gz
inst/extdata/signatures.txt
inst/extdata/simple_somatic_mutation.open.ESCA-CN.sample.tsv.gz
inst/extdata/tcga_cohort.txt.gz
inst/extdata/tcga_laml.maf.gz
inst/extdata/tcga_laml_fab_annotation.txt
inst/extdata/variants.hg19_multianno.txt
inst/extdata/variants.tsv
maftools.Rproj
man
man/GISTIC-class.Rd
man/MAF-class.Rd
man/annovarToMaf.Rd
man/coOncoplot.Rd
man/extractSignatures.Rd
man/forestPlot.Rd
man/geneCloud.Rd
man/genesToBarcodes.Rd
man/getCytobandSummary.Rd
man/getFields.Rd
man/getGeneSummary.Rd
man/getSampleSummary.Rd
man/gisticPlot.Rd
man/icgcSimpleMutationToMAF.Rd
man/inferHeterogeneity.Rd
man/lollipopPlot.Rd
man/mafCompare.Rd
man/mafSurvival.Rd
man/math.score.Rd
man/mutExclusive.Rd
man/oncodrive.Rd
man/oncoplot.Rd
man/oncostrip.Rd
man/oncotate.Rd
man/pancanComparision.Rd
man/pfamDomains.Rd
man/plotCBSsegments.Rd
man/plotClusters.Rd
man/plotGisticResults.Rd
man/plotOncodrive.Rd
man/plotSignatures.Rd
man/plotTiTv.Rd
man/plotVaf.Rd
man/plotmafSummary.Rd
man/prepareMutSig.Rd
man/rainfallPlot.Rd
man/read.maf.Rd
man/readGistic.Rd
man/subsetMaf.Rd
man/tcgaCompare.Rd
man/titv.Rd
man/trinucleotideMatrix.Rd
man/vcr.Rd
man/write.GisticSummary.Rd
man/write.mafSummary.Rd
vignettes
vignettes/maftools.Rmd
maftools documentation built on May 25, 2017, 2:03 a.m.