Package: mutSignatures 2.1.5
mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs
Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes. This computational framework is aimed at deciphering DNA mutational signatures operating in cancer. The framework includes modules that support raw data import and processing, mutational signature extraction, and results interpretation and visualization. The framework accepts widely used file formats storing information about DNA variants, such as Variant Call Format files. The framework performs Non-Negative Matrix Factorization to extract mutational signatures explaining the observed set of DNA mutations. Bootstrapping is performed as part of the analysis. The framework supports parallelization and is optimized for use on multi-core systems. The software was described by Fantini D et al (2020) <doi:10.1038/s41598-020-75062-0> and is based on a custom R-based implementation of the original MATLAB WTSI framework by Alexandrov LB et al (2013) <doi:10.1016/j.celrep.2012.12.008>.
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mutSignatures_2.1.5.tar.gz
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mutSignatures.pdf |mutSignatures.html✨
mutSignatures/json (API)
| # Install 'mutSignatures' in R: |
| install.packages('mutSignatures', repos = c('https://dami82.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dami82/mutsignatures/issues
- mutSigData - Input Data and Examples for Running Mutational Signatures Analyses
Last updated 2 years agofrom:ad40601826. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 09 2024 |
| R-4.5-win | OK | Sep 09 2024 |
| R-4.5-linux | OK | Sep 09 2024 |
| R-4.4-win | OK | Sep 09 2024 |
| R-4.4-mac | OK | Sep 09 2024 |
| R-4.3-win | OK | Sep 09 2024 |
| R-4.3-mac | OK | Sep 09 2024 |
Exports:as.data.frameas.listas.matrixas.mutation.countsas.mutation.signaturesas.mutsign.exposuresattachContextattachMutTypecbind2coerceObjcountMutTypesdecipherMutationalProcessesextractXvarlinkDatafilterSNVfrequencizegetCosmicSignaturesgetCountsgetFwkParamgetMutationTypesgetSampleIdentifiersgetSignatureIdentifiersimportVCFfilesmatchSignaturesmsigPlotplotMutTypeProfileplotSignExposuresprelimProcessAssessprocessVCFdataremoveMismatchMutresolveMutSignaturesrevComplsetFwkParamsetMutClusterParamssetSignatureNamessilhouetteMLBsimplifySignaturessortByMutationstable2df
Dependencies:cliclustercodetoolscolorspacedoParallelfansifarverforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpracmaproxyR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Decipher Mutational Signatures from Somatic Mutational Catalogs. | mutSignatures-package |
| Subset a mutationCounts-class object. | [,mutationCounts,numeric,ANY,ANY-method [,mutationCounts,numeric-method |
| Subset a mutationSignatures-class object. | [,mutationSignatures,numeric,ANY,ANY-method [,mutationSignatures,numeric-method |
| Subset a mutSignExposures-class object. | [,mutSignExposures,numeric,ANY,ANY-method [,mutSignExposures,numeric-method |
| Convert a mutationCounts object to data.frame. | as.data.frame,mutationCounts-method |
| Convert a mutationSignatures object to data.frame. | as.data.frame,mutationSignatures-method |
| Convert and/or transpose a mutSignExposures object to data.frame. | as.data.frame,mutSignExposures-method |
| Convert a mutationSignatures object to list. | as.list,mutationSignatures-method |
| Convert a mutFrameworkParams object to list. | as.list,mutFrameworkParams-method |
| Convert a mutationCounts object to matrix. | as.matrix,mutationCounts-method |
| Method as.mutation.counts. | as.mutation.counts as.mutation.counts,data.frame,ANY,ANY-method as.mutation.counts,data.frame-method |
| Method as.mutation.signatures. | as.mutation.signatures as.mutation.signatures,data.frame-method |
| Method as.mutsign.exposures. | as.mutsign.exposures as.mutsign.exposures,data.frame,logical-method |
| Attach Nucleotide Context. | attachContext |
| Attach Mutation Types. | attachMutType |
| Combine two mutationSignatures-class objects. | cbind2 cbind2,mutationSignatures,mutationSignatures-method |
| Method coerceObj. | coerceObj coerceObj,data.frame,character-method coerceObj,mutationCounts,character-method coerceObj,mutationSignatures,character-method coerceObj,mutFrameworkParams,character-method coerceObj,mutSignExposures,character-method |
| Count Mutation Types. | countMutTypes |
| Decipher Mutational Processes Contributing to a Collection of Genomic Mutations. | decipherMutationalProcesses |
| Extract Variants from XvarlinkData. | extractXvarlinkData |
| Filter Single Nucleotide Variants. | filterSNV |
| Convert Mutation COunts to PerMille Frequencies. | frequencize |
| Obtain COSMIC mutational Signatures. | getCosmicSignatures |
| Method getCounts. | getCounts getCounts,mutationCounts-method |
| Method getFwkParam. | getFwkParam getFwkParam,mutFrameworkParams,character-method |
| Method getMutationTypes. | getMutationTypes getMutationTypes,mutationCounts-method getMutationTypes,mutationSignatures-method |
| Method getSampleIdentifiers. | getSampleIdentifiers getSampleIdentifiers,mutationCounts-method getSampleIdentifiers,mutSignExposures-method |
| Method getSignatureIdentifiers. | getSignatureIdentifiers getSignatureIdentifiers,mutationSignatures-method getSignatureIdentifiers,mutSignExposures-method |
| Import Mutation data from VCF files. | importVCFfiles |
| Match Mutational Signatures. | matchSignatures |
| Method msigPlot. | msigPlot msigPlot,mutationCounts-method msigPlot,mutationSignatures-method msigPlot,mutSignExposures-method |
| Class mutationCounts. | initialize,mutationCounts-method mutationCounts-class |
| Class mutationSignatures. | initialize,mutationSignatures-method mutationSignatures-class |
| Class mutFrameworkParams. | initialize,mutFrameworkParams-method mutFrameworkParams-class |
| Input Data and Examples for Running Mutational Signatures Analyses | mutSigData |
| Class mutSignExposures. | initialize,mutSignExposures-method mutSignExposures-class |
| Plot Mutation Signature Profiles. | plotMutTypeProfile |
| Plot Signature Exposure Profiles. | plotSignExposures |
| Run a Preliminary Process Assess analysis. | prelimProcessAssess |
| Process VCF data. | processVCFdata |
| Remove Mismatched Mutations. | removeMismatchMut |
| Resolve Mutation Signatures. | resolveMutSignatures |
| Compute Reverse Complement sequences. | revCompl |
| Method setFwkParam. | setFwkParam setFwkParam,mutFrameworkParams,character,ANY-method setFwkParam,mutFrameworkParams,character-method |
| Set Parameters for Extracting Mutational Signatures. | setMutClusterParams |
| Method setSignatureNames. | setSignatureNames setSignatureNames,mutationSignatures,character-method |
| Show method of the mutationCounts Class. | print,mutationCounts-method show,mutationCounts-method |
| Show method of the mutationSignatures Class. | print,mutationSignatures-method show,mutationSignatures-method |
| Show method of the mutFrameworkParams Class. | print,mutFrameworkParams-method show,mutFrameworkParams-method |
| Show method of the mutSignExposures Class. | print,mutSignExposures-method show,mutSignExposures-method |
| Silhouette Analysis. | silhouetteMLB |
| Simplify Mutational Signatures. | simplifySignatures |
| Sort Data by Mutation Type. | sortByMutations |
| Table Mutation Types by Sample. | table2df |
