maftools: Summarize, Analyze and Visualize MAF files

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("maftools")
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
Version1.0.55
https://github.com/PoisonAlien/maftools

View on Bioconductor

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).

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.

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...

readGistic: Read and summarize gistic output.

read.maf: Read MAF files.

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.

Functions

annovarToMaf Man page
coOncoplot Man page
extractSignatures Man page
forestPlot Man page
geneCloud Man page
genesToBarcodes Man page
getCytobandSummary Man page
getCytobandSummary,GISTIC-method Man page
getFields Man page
getFields,MAF-method Man page
getGeneSummary Man page
getGeneSummary,GISTIC-method Man page
getGeneSummary,MAF-method Man page
getSampleSummary Man page
getSampleSummary,GISTIC-method Man page
getSampleSummary,MAF-method Man page
GISTIC Man page
GISTIC-class Man page
gisticPlot Man page
icgcSimpleMutationToMAF Man page
inferHeterogeneity Man page
lollipopPlot Man page
MAF Man page
MAF-class Man page
mafCompare Man page
math.score Man page
mutExclusive Man page
oncodrive Man page
oncoplot Man page
oncostrip Man page
oncotate Man page
pfamDomains Man page
plotCBSsegments Man page
plotClusters Man page
plotGisticResults Man page
plotmafSummary Man page
plotOncodrive Man page
plotSignatures Man page
plotTiTv Man page
plotVaf Man page
rainfallPlot Man page
readGistic Man page
read.maf Man page
subsetMaf Man page
titv Man page
trinucleotideMatrix Man page
vcr Man page
write.GisticSummary Man page
write.mafSummary Man page

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/maf_methods.R R/mathScore.R R/mutExclusive.R R/oncodrive.R R/oncoplot.R R/oncostrip.R R/oncotate.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/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/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/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/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_laml.maf.gz
inst/extdata/tcga_laml_fab_annotation.txt
inst/extdata/variants.hg19_multianno.txt
inst/extdata/variants.tsv
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/math.score.Rd man/mutExclusive.Rd man/oncodrive.Rd man/oncoplot.Rd man/oncostrip.Rd man/oncotate.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/rainfallPlot.Rd man/read.maf.Rd man/readGistic.Rd man/subsetMaf.Rd man/titv.Rd man/trinucleotideMatrix.Rd man/vcr.Rd man/write.GisticSummary.Rd man/write.mafSummary.Rd
vignettes
vignettes/maftools.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.