Decipher Mutational Signatures from Somatic Mutational Catalogs

Documentation for package ‘mutSignatures’ version 1.2

mutSignatures-package	Computational Framework for Deciphering Cancer Mutational Signatures
addWeak	Add Weak Mutation Types
bootstrapCancerGenomes	Bootstrap a Mutation Count Matrix
citation	Print Citation Information
decipherMutationalProcesses	Decipher Mutational Processes Contributing to a Collection of Genomic Mutations
deconvoluteMutCounts	Deconvolute Mutation Counts
do.nmf	Perform Non-negative Matrix Factorization
evaluateStability	Evaluate Results Stability
extractSignatures	Extract Signatures from Genomic Mutational Catalogs
filterOutIterations	Remove Iterations that Generated Outlier Results
getTestRunArgs	Generate Arguments for Running Examples and Mock Runs
leadZeros	Add Leading Zeros to a Number
mutSignatures	Computational Framework for Deciphering Cancer Mutational Signatures
plotSignatureExposures	Generate Plot Signature
removeWeak	Remove Mutation Types Not Meeting the Threshold
setMutClusterParams	Set Parameters for Extracting Mutational Signatures
setMutCountObject	Create a Mutation Count Object Suitable for Signatures Extraction
silhouetteMLB	Silhouette Analysis