MPAgenomics: an R package for multi-patient analysis of genomic markers

Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures. MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic ma...

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Bibliographic Details
Published in:BMC bioinformatics 2014-12, Vol.15 (1), p.394-394, Article 394
Main Authors: Grimonprez, Quentin, Celisse, Alain, Blanck, Samuel, Cheok, Meyling, Figeac, Martin, Marot, Guillemette
Format: Article
Language:English
Subjects:
Arrays
Bioinformatics
DNA Copy Number Variations
Gain
Genes
Genetic aspects
Genetic Markers
Genomes
High-Throughput Nucleotide Sequencing - methods
Humans
Markers
Medical research
Methods
Nucleotides
Packages
Packaging
Polymorphism, Single Nucleotide
Programming languages
Regression
Segmentation
Sequence Analysis, DNA - methods
Single nucleotide polymorphisms
Software
Studies
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Description
Summary:Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures. 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. MPAgenomics provides an easy tool to analyze data from SNP arrays in R. The R-package MPAgenomics is available on CRAN.
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-014-0394-y