title: MPAgenomics: an R package for multi-patient analysis of genomic markers.
abstract: BACKGROUND
  Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures.
  
  
  RESULTS
  MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic markers from multi-patient copy number and SNP data profiles. It provides wrappers from commonly used packages to streamline their repeated (sometimes difficult) manipulation, offering an easy-to-use pipeline for beginners in R.The segmentation of successive multiple profiles (finding losses and gains) is performed with an automatic choice of parameters involved in the wrapped packages. Considering multiple profiles in the same time, MPAgenomics wraps efficient penalized regression methods to select relevant markers associated with a given outcome.
  
  
  CONCLUSIONS
  MPAgenomics provides an easy tool to analyze data from SNP arrays in R. The R-package MPAgenomics is available on CRAN.
authors.affiliation: MODAL team, Inria Lille-Nord Europe, Villeneuve-d'Ascq, France. quentin.grimonprez@inria.fr.
authors.forename: Quentin
authors.initials: Q
authors.lastname: Grimonprez
authors.forename: Alain
authors.initials: A
authors.lastname: Celisse
authors.forename: Samuel
authors.initials: S
authors.lastname: Blanck
authors.forename: Meyling
authors.initials: M
authors.lastname: Cheok
authors.forename: Martin
authors.initials: M
authors.lastname: Figeac
authors.forename: Guillemette
authors.initials: G
authors.lastname: Marot
mesh_terms: D056915:DNA Copy Number Variations; D005819:Genetic Markers; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D005819:Genetic Markers