2014/01/20 by Quentin Grimonprez, Grimonprez, Quentin, Alain Celisse +7
Biochemistry, Genetics and Molecular Biology · Mathematics · #Applications (stat.AP) #FOS: Biological sciences #FOS: Computer and information sciences #Quantitative Methods (q-bio.QM) #q-bio.QM #stat.AP
paper · pdf · doi:10.48550/arxiv.1401.5035
arxiv created 2014/01/20 · arxiv updated 2014/01/21
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.