Skip to Main content Skip to Navigation
Journal articles

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
Inria Lille - Nord Europe, LPP - Laboratoire Paul Painlevé - UMR 8524, METRICS - Evaluation des technologies de santé et des pratiques médicales - ULR 2694, Polytech Lille - École polytechnique universitaire de Lille, Université de Lille, Sciences et Technologies
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.
Document type :
Journal articles
Complete list of metadata

Cited literature [23 references]  Display  Hide  Download

https://hal.inria.fr/hal-00933614
Contributor : Nadia Taibi <>
Submitted on : Wednesday, January 14, 2015 - 10:27:47 AM
Last modification on : Friday, January 22, 2021 - 1:18:04 PM
Long-term archiving on: : Friday, September 11, 2015 - 6:44:02 AM

File

s12859-014-0394-y.pdf
Publisher files allowed on an open archive

Identifiers

Collections

Citation

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⟩

Share

Metrics

Record views

537

Files downloads

1005