ebGenotyping: Genotyping and SNP Detection using Next Generation Sequencing Data

Genotyping the population using next generation sequencing data is essentially important for the rare variant detection. In order to distinguish the genomic structural variation from sequencing error, we propose a statistical model which involves the genotype effect through a latent variable to depict the distribution of non-reference allele frequency data among different samples and different genome loci, while decomposing the sequencing error into sample effect and positional effect. An ECM algorithm is implemented to estimate the model parameters, and then the genotypes and SNPs are inferred based on the empirical Bayes method.

Version: 2.0.1
Published: 2016-04-13
DOI: 10.32614/CRAN.package.ebGenotyping
Author: Na You and Gongyi Huang
Maintainer: Gongyi Huang <53hgy at 163.com>
License: GPL-2
NeedsCompilation: no
CRAN checks: ebGenotyping results


Reference manual: ebGenotyping.pdf


Package source: ebGenotyping_2.0.1.tar.gz
Windows binaries: r-devel: ebGenotyping_2.0.1.zip, r-release: ebGenotyping_2.0.1.zip, r-oldrel: ebGenotyping_2.0.1.zip
macOS binaries: r-release (arm64): ebGenotyping_2.0.1.tgz, r-oldrel (arm64): ebGenotyping_2.0.1.tgz, r-release (x86_64): ebGenotyping_2.0.1.tgz, r-oldrel (x86_64): ebGenotyping_2.0.1.tgz
Old sources: ebGenotyping archive


Please use the canonical form https://CRAN.R-project.org/package=ebGenotyping to link to this page.