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mutSignatures (version 2.1.1)

Decipher Mutational Signatures from Somatic Mutational Catalogs

Description

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) and is based on a custom R-based implementation of the original MATLAB WTSI framework by Alexandrov LB et al (2013) .

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Version

Install

install.packages('mutSignatures')

Monthly Downloads

239

Version

2.1.1

License

GPL-2

Maintainer

Damiano Fantini

Last Published

November 9th, 2020

Functions in mutSignatures (2.1.1)

custom_cssls

Custom CSSLS.
bootstrapCancerGenomes

Bootstrap a Mutation Count Matrix.
attachMutType

Attach Mutation Types.
custom_fcnnls

Custom Fast Combinatorial Nonnegative Least-Square.
getCounts

Method getCounts.
attachContext

Attach Nucleotide Context.
getCosmicSignatures

Obtain COSMIC mutational Signatures.
as.mutsign.exposures

Method as.mutsign.exposures.
getFwkParam

Method getFwkParam.
coerceObj

Method coerceObj.
filterSNV

Filter Single Nucleotide Variants.
decipherMutationalProcesses

Decipher Mutational Processes Contributing to a Collection of Genomic Mutations.
countMutTypes

Count Mutation Types.
frequencize

Convert Mutation COunts to PerMille Frequencies.
show,mutationCounts-method

Show method of the mutationCounts Class.
getMutationTypes

Method getMutationTypes.
importVCFfiles

Import Mutation data from VCF files.
getTestRunArgs

Generate Arguments for Running Examples and Mock Runs.
evaluateStability

Evaluate Results Stability.
getSampleIdentifiers

Method getSampleIdentifiers.
silhouetteMLB

Silhouette Analysis.
getSignatureIdentifiers

Method getSignatureIdentifiers.
show,mutationSignatures-method

Show method of the mutationSignatures Class.
deconvoluteMutCounts

Deconvolute Mutation Counts.
as.list,mutFrameworkParams-method

Convert a mutFrameworkParams object to list.
setMutClusterParams

Set Parameters for Extracting Mutational Signatures.
plotMutTypeProfile

Plot Mutation Signature Profiles.
processVCFdata

Process VCF data.
mutationSignatures-class

Class mutationSignatures.
removeMismatchMut

Remove Mismatched Mutations.
mutSignatures-package

Decipher Mutational Signatures from Somatic Mutational Catalogs.
mutationCounts-class

Class mutationCounts.
revCompl

Compute Reverse Complement sequences.
setFwkParam

Method setFwkParam.
cbind2

Combine two mutationSignatures-class objects.
resolveMutSignatures

Resolve Mutation Signatures.
msigPlot

Method msigPlot.
extractSignatures

Extract Signatures from Genomic Mutational Catalogs.
mutFrameworkParams-class

Class mutFrameworkParams.
show,mutFrameworkParams-method

Show method of the mutFrameworkParams Class.
extractXvarlinkData

Extract Variants from XvarlinkData.
chihJenNMF

Perform Non-negative Matrix Factorization using Chih-Jen Lin's Algotithm.
filterOutIterations

Remove Iterations that Generated Outlier Results.
matchSignatures

Match Mutational Signatures.
[,mutationSignatures,numeric,ANY,ANY-method

Subset a mutationSignatures-class object.
plotSignExposures

Plot Signature Exposure Profiles.
leadZeros

Add Leading Zeros to Numbers.
mutSigData

Input Data and Examples for Running Mutational Signatures Analyses
removeWeak

Remove Mutation Types Not Meeting the Threshold.
table2df

Table Mutation Types by Sample.
[,mutSignExposures,numeric,ANY,ANY-method

Subset a mutSignExposures-class object.
[,mutationCounts,numeric,ANY,ANY-method

Subset a mutationCounts-class object.
prelimProcessAssess

Run a Preliminary Process Assess analysis.
mutSignExposures-class

Class mutSignExposures.
simplifySignatures

Simplify Mutational Signatures.
show,mutSignExposures-method

Show method of the mutSignExposures Class.
sortByMutations

Sort Data by Mutation Type.
as.data.frame,mutSignExposures-method

Convert and/or transpose a mutSignExposures object to data.frame.
as.mutation.signatures

Method as.mutation.signatures.
addWeak

Add Weak Mutation TYpes
as.data.frame,mutationSignatures-method

Convert a mutationSignatures object to data.frame.
as.list,mutationSignatures-method

Convert a mutationSignatures object to list.
as.mutation.counts

Method as.mutation.counts.
as.data.frame,mutationCounts-method

Convert a mutationCounts object to data.frame.
alexaNMF

Perform Non-negative Matrix Factorization using Brunet's Algotithm.
as.matrix,mutationCounts-method

Convert a mutationCounts object to matrix.