maftools: Summarize, Analyze and Visualize MAF files

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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.

Author
Anand Mayakonda <anand_mt@hotmail.com>
Date of publication
None
Maintainer
Anand Mayakonda <anand_mt@hotmail.com>
License
MIT + file LICENSE
Version
1.0.20
URLs

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.

Files in this package

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