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ModSaRa: a computationally efficient R package for CNV identification.

ABSTRACT: 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.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 .heping.zhang@yale.edu.Supplementary data are available at Bioinformatics online.

SUBMITTER: Xiao F

PROVIDER: S-EPMC5860124 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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modSaRa: a computationally efficient R package for CNV identification.

Xiao Feifei F Niu Yue Y Hao Ning N Xu Yanxun Y Jin Zhilin Z Zhang Heping H

Bioinformatics (Oxford, England) 20170801 15

<h4>Summary</h4>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 accur ...[more]

PMID: 28453611

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