Identifying somatic signatures of single nucleotide variants. This package provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.
The 'SomaticSignatures' package offers the framework for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments. In the concept of mutational signatures, a base change resulting from an SNV is regarded in term of motifs which embeds the variant in the context of the surrounding genomic sequence. Based on the frequency of such motifs across samples, mutational signatures and their occurrance in the samples can be estimated. An introduction into the methodology and a use case are illustrated in the vignette of this package.
Julian Gehring, Bernd Fischer, Michael Lawrence, Wolfgang Huber: SomaticSignatures: Inferring Mutational Signatures from Single Nucleotide Variants. 2015, bioRxiv preprint, http://dx.doi.org/10.1101/010686
Maintainer: Julian Gehring, EMBL Heidelberg <[email protected]>
Nik-Zainal, Serena, Ludmil B. Alexandrov, David C. Wedge, Peter Van Loo, Christopher D. Greenman, Keiran Raine, David Jones, et al. "Mutational Processes Molding the Genomes of 21 Breast Cancers." Cell 149, no. 5 (May 25, 2012): 979-993. doi:10.1016/j.cell.2012.04.024.
Alexandrov, Ludmil B., Serena Nik-Zainal, David C. Wedge, Samuel A. J. R. Aparicio, Sam Behjati, Andrew V. Biankin, Graham R. Bignell, et al. "Signatures of Mutational Processes in Human Cancer." Nature 500, no. 7463 (August 22, 2013): 415-421. doi:10.1038/nature12477.
Gaujoux, Renaud, and Cathal Seoighe. "A Flexible R Package for Nonnegative Matrix Factorization." BMC Bioinformatics 11, no. 1 (July 2, 2010): 367. doi:10.1186/1471-2105-11-367.
Stacklies, Wolfram, Henning Redestig, Matthias Scholz, Dirk Walther, and Joachim Selbig. "pcaMethods - A Bioconductor Package Providing PCA Methods for Incomplete Data." Bioinformatics 23, no. 9 (May 1, 2007): 1164-1167. doi:10.1093/bioinformatics/btm069.
vignette(package = "SomaticSignatures")
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