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

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 (s...

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Bibliographic Details
Published in:BMC bioinformatics 2014-12, Vol.15
Main Authors: Grimonprez, Quentin, Celisse, Alain, Blanck, Samuel, Cheok, Meyling, Figeac, Martin, Marot, Guillemette
Format: Article
Language:English
Subjects:
Life Sciences
Quantitative Methods
Online Access:Get full text
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Description
Summary: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.
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-014-0394-y