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MPAgenomics : An R package for multi-patients analysis of genomic markers
- Source :
- BMC Bioinformatics, BMC Bioinformatics, BioMed Central, 2014, 15, pp.394. ⟨10.1186/s12859-014-0394-y⟩, BMC Bioinformatics, 2014, 15, pp.394. ⟨10.1186/s12859-014-0394-y⟩
- Publication Year :
- 2014
- Publisher :
- arXiv, 2014.
-
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.
- Subjects :
- FOS: Computer and information sciences
computer.software_genre
Quantitative Biology - Quantitative Methods
01 natural sciences
Biochemistry
010104 statistics & probability
Software
Structural Biology
Segmentation
calling
Quantitative Methods (q-bio.QM)
Multi-patient analysis
0303 health sciences
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Applied Mathematics
Multi patient analysis
SNP array
Genomic markers selection
Calling
Normalization
High-Throughput Nucleotide Sequencing
multi patient analysis
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Computer Science Applications
normalization
Marker selection
Data mining
Genetic Markers
Normalization (statistics)
DNA Copy Number Variations
Segmentation of genomic data
genomic markers selection
Biology
Polymorphism, Single Nucleotide
Statistics - Applications
03 medical and health sciences
Humans
Applications (stat.AP)
0101 mathematics
Molecular Biology
030304 developmental biology
Penalized regression
SNP arrays
business.industry
R package
segmentation
Sequence Analysis, DNA
Pipeline (software)
FOS: Biological sciences
business
computer
Subjects
Details
- ISSN :
- 14712105
- Database :
- OpenAIRE
- Journal :
- BMC Bioinformatics, BMC Bioinformatics, BioMed Central, 2014, 15, pp.394. ⟨10.1186/s12859-014-0394-y⟩, BMC Bioinformatics, 2014, 15, pp.394. ⟨10.1186/s12859-014-0394-y⟩
- Accession number :
- edsair.doi.dedup.....23fd5ed41e25369fce35c8d6eda6b579
- Full Text :
- https://doi.org/10.48550/arxiv.1401.5035