This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signaturespecific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.
Package details 


Author  Daniel Huebschmann, Lea JoppSaile, Carolin Andresen, Zuguang Gu and Matthias Schlesner 
Bioconductor views  BiologicalQuestion Clustering DNASeq GenomicVariation Sequencing SomaticMutation StatisticalMethod Visualization 
Maintainer  Daniel Huebschmann <huebschmann.daniel@googlemail.com> 
License  GPL3 
Version  1.16.0 
Package repository  View on Bioconductor 
Installation 
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