Package: maftools 2.29.0

Anand Mayakonda

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.

Authors:Anand Mayakonda [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
maftools/json (API)

# Install 'maftools' in R:
install.packages('maftools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/poisonalien/maftools/issues

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library

On BioConductor:maftools-2.29.0(bioc 3.24)maftools-2.28.0(bioc 3.23)

datarepresentationdnaseqvisualizationdrivermutationvariantannotationfeatureextractionclassificationsomaticmutationsequencingfunctionalgenomicssurvivalbioinformaticscancer-genome-atlascancer-genomicsgenomicsmaf-filestcgacurlbzip2xz-utilszlib

13.41 score 495 stars 12 packages 1.6k scripts 288 mentions 83 exports 18 dependencies

Last updated from:972fe51fb7. Checks:1 ERROR, 4 WARNING, 1 OK, 7 NOTE, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR303
linux-devel-arm64WARNING386
linux-devel-x86_64WARNING351
source / vignettesOK433
linux-release-arm64WARNING407
linux-release-x86_64WARNING370
macos-release-arm64NOTE249
macos-release-x86_64NOTE513
macos-oldrel-arm64NOTE231
macos-oldrel-x86_64NOTE436
windows-develNOTE358
windows-releaseNOTE347
windows-oldrelNOTE323
wasm-releaseFAIL533

Exports:annovarToMafbamreadcountscancerhotspotscancerhotspotsAggrclinicalEnrichmentcoBarplotcoGisticChromPlotcompareSignaturescoOncoplotdrugInteractionsestimateSignaturesextractSignaturesfilterMafforestPlotgenesToBarcodesgenotypeMatrixgetClinicalDatagetCytobandSummarygetFieldsgetGeneSummarygetSampleSummarygisticBubblePlotgisticChromPlotgisticComparegisticOncoPlotgtMarkersicgcSimpleMutationToMAFinferHeterogeneityintersectMAFlollipopPlotlollipopPlot2MAFmaf2maemafbarplotmafComparemafSummarymafSurvGroupmafSurvivalmath.scoremerge_mafsmutCountMatrixoncodriveoncoplotoncostrippathwayspfamDomainsplotApobecDiffplotCBSsegmentsplotClustersplotCopheneticplotEnrichmentResultsplotmafSummaryplotMosdepthplotMosdepth_tplotOncodriveplotPathwaysplotProteinplotSignaturesplotTiTvplotVafprepareMutSigprepAscatprepAscat_trainfallPlotread.mafreadGisticsampleSwapssegmentLogRsegSummarizesetdiffMAFsignatureEnrichmentsomaticInteractionssubsetMafsurvGrouptcgaAvailabletcgaComparetcgaLoadtitvtmbtrinucleotideMatrixvafComparewrite.GisticSummarywrite.mafSummary

Dependencies:clidata.tableDNAcopyfarvergluegtablelabelinglatticelifecycleMatrixpheatmapR6RColorBrewerRhtslibrlangscalessurvivalviridisLite

Customizing oncoplots
Including Transition/Transversions into oncoplot | Changing colors for variant classifications | Including copy number data into oncoplots. | GISTIC results | Custom copy-number table | Bar plots | Including annotations | Highlighting samples | Group by Pathways | Oncogenic siganlling pathways | Biological processes of known drivers | Custom pathway list | Collapse pathways | Combining everything | SessionInfo
Rendered fromoncoplots.Rmdusingknitr::rmarkdown

Last update: 2024-10-16
Started: 2019-04-20

maftools : Summarize, Analyze and Visualize MAF Files
Introduction | Citation | Generating MAF files | MAF field requirements | Installation | Overview of the package | Reading and summarizing maf files | Required input files | Reading MAF files. | MAF object | Visualization | Plotting MAF summary. | Oncoplots | Drawing oncoplots | Transition and Transversions. | Lollipop plots for amino acid changes | MAF as an input | Custom data as an input | Rainfall plots | Compare mutation load against TCGA cohorts | Plotting VAF | Processing copy-number data | Reading and summarizing gistic output files. | Visualizing gistic results. | genome plot | Co-gisticChromPlot | Bubble plot | oncoplot | CBS segments | Summarizing chromosomal arm level CN | Visualizing CBS segments | Analysis | Somatic Interactions | Detecting cancer driver genes based on positional clustering | Adding and summarizing pfam domains | Survival analysis | Mutation in any given genes | Predict genesets associated with survival | Comparing two cohorts (MAFs) | Forest plots | Co-onco plots | Co-bar plots | Lollipop plot-2 | Clinical enrichment analysis | Drug-Gene Interactions | Oncogenic Signaling Pathways | Tumor heterogeneity and MATH scores | Heterogeneity in tumor samples | Ignoring variants in copy number altered regions | Mutational Signatures | APOBEC Enrichment estimation. | Differences between APOBEC enriched and non-enriched samples | Signature analysis | Variant Annotations | Converting annovar output to MAF | Converting ICGC Simple Somatic Mutation Format to MAF | Prepare MAF file for MutSigCV analysis | Set operations | Subsetting MAF | Specifying queries and controlling output fields. | Subsetting by clinical data | Sample swap identification | TCGA cohorts | Available cohorts | Loading a TCGA cohort | MultiAssayExperiment | Useful links and tools | References | Session Info | Support and acknowledgments | Github | Acknowledgements
Rendered frommaftools.Rmdusingknitr::rmarkdown

Last update: 2024-09-11
Started: 2016-04-02

Copy number analysis
Introduction | Van Loo P, Nordgard SH, Lingjærde OC, et al. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A. 2010;107(39):16910-16915. doi:10.1073/pnas.1009843107 | Step-1: Get nucleotide counts for genetic markers | Step-2: Prepare input files for ASCAT with prepAscat() | Tumor-Normal pair | Tumor only | CBS segmentation | Processing Mosdepth output | Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics. 2018;34(5):867-868. doi:10.1093/bioinformatics/btx699 | Tumor normal pair | Session Info
Rendered fromcnv_analysis.Rmdusingknitr::rmarkdown

Last update: 2022-04-08
Started: 2022-04-05

Personlaized cancer report
Genotype cancer hotspots | Fetch readcounts for targetted loci
Rendered fromcancer_hotspots.Rmdusingknitr::rmarkdown

Last update: 2022-04-06
Started: 2021-04-04

Readme and manuals

Help Manual

Help pageTopics
Converts annovar annotations into MAF.annovarToMaf
extract nucleotide counts for targeted variants from the BAM file.bamreadcounts
Genotype known cancer hotspots from the tumor BAM filecancerhotspots
Aggregate cancerhotspots reportscancerhotspotsAggr
Performs mutational enrichment analysis for a given clinical feature.clinicalEnrichment
Draw two barplots side by side for cohort comparision.coBarplot
Co-plot version of gisticChromPlot()coGisticChromPlot
Compares identified denovo mutational signatures to known COSMIC signaturescompareSignatures
Draw two oncoplots side by side for cohort comparision.coOncoplot
Drug-Gene InteractionsdrugInteractions
Estimate number of signatures based on cophenetic correlation metricestimateSignatures
Extract mutational signatures from trinucleotide context.extractSignatures
Filter MAF objectsfilterMaf
Draw forest plot for differences betweeen cohorts.forestPlot
Extracts Tumor Sample Barcodes where the given genes are mutated.genesToBarcodes
Creates a Genotype Matrix for every variantgenotypeMatrix
extract annotations from MAF objectgetClinicalData getClinicalData,MAF-method
extract cytoband summary from GISTIC objectgetCytobandSummary getCytobandSummary,GISTIC-method
extract available fields from MAF objectgetFields getFields,MAF-method
extract gene summary from MAF or GISTIC objectgetGeneSummary getGeneSummary,GISTIC-method getGeneSummary,MAF-method
extract sample summary from MAF or GISTIC objectgetSampleSummary getSampleSummary,GISTIC-method getSampleSummary,MAF-method
Class GISTICGISTIC GISTIC-class
Plot gistic results as a bubble plotgisticBubblePlot
Plot gistic results along linearized chromosomegisticChromPlot
compare two GISTIC objectsgisticCompare
Plot gistic results.gisticOncoPlot
Extract read counts from genetic markers for ASCAT analysisgtMarkers
Converts ICGC Simple Somatic Mutation format file to MAFicgcSimpleMutationToMAF
Clusters variants based on Variant Allele Frequencies (VAF).inferHeterogeneity
Draws lollipop plot of amino acid changes on to Protein structure.lollipopPlot
Compare two lollipop plotslollipopPlot2
Construct an MAF objectMAF
Class MAFMAF-class
Convert MAF to MultiAssayExperiment objectmaf2mae
Creates a bar plotmafbarplot
compare two cohorts (MAF).mafCompare
Summary statistics of MAFmafSummary
Performs survival analysis for a genesetmafSurvGroup
Performs survival analysismafSurvival
calculates MATH (Mutant-Allele Tumor Heterogeneity) score.math.score
Merge multiple mafs into single MAFmerge_mafs
Generates count matrix of mutations.mutCountMatrix
Detect cancer driver genes based on positional clustering of variants.oncodrive
draw an oncoplotoncoplot
draw an oncostrip similar to cBioportal oncoprinter output.oncostrip
Enrichment of known oncogenic or custom pathwayspathways
pfam domain annotation and summarization.pfamDomains
Plot differences between APOBEC enriched and non-APOBEC enriched samples.plotApobecDiff
Plots segmented copy number data.plotCBSsegments
Plot density plots from clutering results.plotClusters
Draw an elbow plot of cophenetic correlation metric.plotCophenetic
Plots results from clinicalEnrichment analysisplotEnrichmentResults
Plots maf summary.plotmafSummary
Plot results from mosdepth output for Tumor/Normal pairplotMosdepth
Plot results from mosdepth outputplotMosdepth_t
Plots results from 'oncodrive'plotOncodrive
Plot oncogenic pathwaysplotPathways
Display protein domainsplotProtein
Plots decomposed mutational signaturesplotSignatures
Plot Transition and Trasnversion ratios.plotTiTv
Plots vaf distribution of genesplotVaf
Prepares MAF file for MutSig analysis.prepareMutSig
Prepare input files for ASCATprepAscat
Prepare input files for ASCAT tumor only samplesprepAscat_t
Rainfall plot to display hyper mutated genomic regions.rainfallPlot
Read MAF files.read.maf
Read and summarize gistic output.readGistic
Identify sample swaps and similaritiessampleSwaps
Segment and plot log ratio values with DNACopysegmentLogR
Summarize CBS segmentation resultssegSummarize
Set Operations for MAF objectsintersectMAF setdiffMAF
Performs sample stratification based on signature contribution and enrichment analysis.signatureEnrichment
Exact tests to detect mutually exclusive, co-occuring and altered genesets.somaticInteractions
Subset MAF objectssubsetMaf
Predict genesets associated with survivalsurvGroup
Prints available TCGA datasetstcgaAvailable
Compare mutation load against TCGA cohortstcgaCompare
Compare genes to known TCGA drivers and their biological pathwaystcgaDriverBP
Loads a TCGA cohorttcgaLoad
Classifies SNPs into transitions and transversionstitv
Estimate Tumor Mutation Burdentmb
Extract single 5' and 3' bases flanking the mutated site for de-novo signature analysis. Also estimates APOBEC enrichment scores.trinucleotideMatrix
compare VAF across two cohortsvafCompare
Writes GISTIC summaries to output tab-delimited text files.write.GisticSummary
Writes maf summaries to output tab-delimited text files.write.mafSummary