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MPAgenomics : An R package for multi-patients analysis of genomic markers

Quentin Grimonprez 1 Alain Celisse 1, 2 Samuel Blanck 1 Meyling Cheok 3 Martin Figeac 4 Guillemette Marot 1, 5 
1 MODAL - MOdel for Data Analysis and Learning
LPP - Laboratoire Paul Painlevé - UMR 8524, Université de Lille, Sciences et Technologies, Inria Lille - Nord Europe, METRICS - Evaluation des technologies de santé et des pratiques médicales - ULR 2694, Polytech Lille - École polytechnique universitaire de Lille
Abstract : MPAgenomics, standing for multi-patients analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation, and (ii) genomic marker selection from multi-patient copy number and SNP data profiles. It provides wrappers from commonly used packages to facilitate their repeated (sometimes difficult) use, offering an easy-to-use pipeline for beginners in R. The segmentation of successive multiple profiles (finding losses and gains) is based on a new automatic choice of influential parameters since default ones were misleading in the original packages. Considering multiple profiles in the same time, MPAgenomics wraps efficient penalized regression methods to select relevant markers associated with a given response.
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Quentin Grimonprez, Alain Celisse, Samuel Blanck, Meyling Cheok, Martin Figeac, et al.. MPAgenomics : An R package for multi-patients analysis of genomic markers. BMC Bioinformatics, BioMed Central, 2014, 15, pp.394. ⟨10.1186/s12859-014-0394-y⟩. ⟨hal-00933614v3⟩

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