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

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Grimonprez, Quentin ^a   Celisse, Alain ^a,b   Blanck, Samuel ^a   Cheok, Meyling ^c   Figeac, Martin ^d   Marot, Guillemette ^a,d  

^a INRIA   (France)

^b UNIVERSITÉ LILLE 1   (France)

^c INSERM   (France)

^d UNIV LILLE   (France)

Author keywords

Marker selection; Multi patient analysis; R package; Segmentation of genomic data; SNP arrays

Indexed keywords

COPY NUMBER; COPY NUMBER VARIATIONS; DATA PROFILES; GENOMIC DATA; MARKER SELECTION; MULTI-PATIENT ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM ARRAYS; SNP ARRAYS;

GENES;

GENETIC MARKER;

COMPUTER PROGRAM; COPY NUMBER VARIATION; DNA SEQUENCE; GENETIC MARKER; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA COPY NUMBER VARIATIONS; GENETIC MARKERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84923860119     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-014-0394-y     Document Type: Article

References (24)

1. LaFramboise T: Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res2009, 37(13):4181-4193.
2. Bengtsson H, Simpson K, Bullard J, Hansen K: aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory. Technical Report 745, Department of Statistics, University of California, Berkeley; 2008.
3. Bengtsson H, Bullard J, Hansen K, Neuvial P, Purdomand E, Robinson M, Simpson K: Aroma project2010. [ http://www.aroma-project.org/ ]
4. Killick R, Eckley I: Changepoint: An R Package for Changepoint Analysis2013. R package version 1.1, [ http://www.lancs.ac.uk/~killick/Pub/KillickEckley2011.pdf ]
5. van de Wiel M, Vosse S: CGHcall: Calling Aberrations for Array CGH Tumor Profiles2012. R package version 2.20.0 [ http://www.bioconductor.org/packages/release/bioc/vignettes/CGHcall/inst/doc/CGHcall.pdf ]
6. Friedman JH, Hastie T, Tibshirani R: Regularization paths for generalized linear models via coordinate descent. J Stat Softw2010, 33(1):1-22.
7. R Core Team: R: A Language and Environment for Statistical Computing, Vienna, Austria: R Foundation for Statistical Computing; 2014. [ http://www.R-project.org/ ]
8. Bengtsson H, Neuvial P, Speed TP: Tumorboost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics2010, 11:245.
9. Bengtsson H, Wirapati P, Speed TP: A single-array preprocessing method for estimating full-resolution raw copys from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics2009, 25(17):2149-2156.
10. Hocking T, Schleiermacher G, Janoueix-Lerosey I, Boeva V, Cappo J, Delattre O, Bach F, Vert J-P: Learning smoothing models of copy number profiles using breakpoint annotations. BMC Bioinformatics2013, 14(1):164.
11. Picard F, Robin S, Lavielle M, Vaisse C, Daudin J-J: A statistical approach for array CGH data analysis. BMC Bioinformatics2005, 6(1):27.
12. Rigaill G: Pruned dynamic programming for optimal multiple change-point detection. arXiv e-print, 2010, arXiv/1004.0887.
13. Killick R, Fearnhead P, Eckley IA: Optimal detection of changepoints with a linear computational cost. J Am Stat Assoc2012, 107(500):1590-1598.
14. Lebarbier E: Detecting multiple change-points in the mean of gaussian process by model selection. Signal Process2005, 85(4):717-736.
15. Birgé L, Massart P: Minimal penalties for gaussian model selection. Probability Theory Related Fields2007, 138(1-2):33-73.
16. Staaf J, Lindgren D, Vallon-Christersson J, Isaksson A, Göransson H, Juliusson G, Rosenquist R, Höglund M, Borg Å, Ringnér M: Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays. Genome Biol2008, 9(9):R136.
17. van de Wiel MA, Kim KI, Vosse SJ, van Wieringen WN, Wilting SM, Ylstra B: CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics2007, 23(7):892-894.
18. Tibshirani R: Regression shrinkage and selection via the lasso. J R Stat Soci Series B1994, 58:267-288.
19. Efron B, Hastie T, Johnstone I, Tibshirani R: Least angle regression. Ann Stat2004, 32:407-499.
20. Ravikumar P, Wainwright M. J, Raskutti G, Yu B: High-dimensional covariance estimation by minimizing l 1 -penalized log-determinant divergence. Electron J Stat2011, 5:935-980.
21. Ishwaran H, Rao JS: Spike and slab variable selection: frequentist and bayesian strategies. Ann Stat2005, 33(2):730-773.
22. Ishwaran H, Rao JS: Generalized ridge regression: geometry and computational solutions when p is larger than n. Technical Report, Department of Public Health Sciences Division of Biostatistics, University of Miami, Miller School of Medecine; 2010.
23. Arlot S, Celisse A: A survey of cross-validation procedures for model selection. Stat Surv2010, 4:40-79.
24. Anscombe FJ: The transformation of poisson, binomial, and negative-binomial data. Biometrika1948, 35(3/4):246-254.