Feifei Xiao1, Yue Niu2, Ning Hao2, Yanxun Xu3, Zhilin Jin3, Heping Zhang4. 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.
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.
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