ebGenotyping: Genotyping and SNP Detection using Next Generation Sequencing Data
Version 2.0.1

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.

Package details

AuthorNa You <youn@mail.sysu.edu.cn> and Gongyi Huang<53hgy@163.com>
Date of publication2016-04-13 09:28:12
MaintainerGongyi Huang<53hgy@163.com>
LicenseGPL-2
Version2.0.1
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("ebGenotyping")

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ebGenotyping documentation built on May 30, 2017, 12:18 a.m.