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Bioinformatics. 2017 Aug 1;33(15):2384-2385. doi: 10.1093/bioinformatics/btx212.

modSaRa: a computationally efficient R package for CNV identification.

Author information

1
Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC 29201, USA.
2
Department of Mathematics, University of Arizona, Tucson, AZ 85721, USA.
3
Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD 21218, USA.
4
Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA.

Abstract

Summary:

Chromosomal copy number variation (CNV) refers to a polymorphism that a DNA segment presents deletion or duplication in the population. The computational algorithms developed to identify this type of variation are usually of high computational complexity. Here we present a user-friendly R package, modSaRa, designed to perform copy number variants identification. The package is developed based on a change-point based method with optimal computational complexity and desirable accuracy. The current version of modSaRa package is a comprehensive tool with integration of preprocessing steps and main CNV calling steps.

Availability and Implementation:

modSaRa is an R package written in R, C ++ and Rcpp and is now freely available for download at http://c2s2.yale.edu/software/modSaRa .

Contact:

heping.zhang@yale.edu.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28453611
PMCID:
PMC5860124
DOI:
10.1093/bioinformatics/btx212
[Indexed for MEDLINE]
Free PMC Article

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