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.

Author
Na You <youn@mail.sysu.edu.cn> and Gongyi Huang<53hgy@163.com>
Date of publication
2016-04-13 09:28:12
Maintainer
Gongyi Huang<53hgy@163.com>
License
GPL-2
Version
2.0.1

View on CRAN

Man pages

ebGenotyping-package
Genotyping and SNP Detection using Next Generation Sequencing...
ecm
Genotyping and SNP Detection using Next Generation Sequencing...
estep
E step
logit
Logit Transformation
mstep
CM steps
my.bisec
Bisection method to find the root
rlogit
Inverse Logit Transformation

Files in this package

ebGenotyping
ebGenotyping/NAMESPACE
ebGenotyping/R
ebGenotyping/R/logit.R
ebGenotyping/R/mstep.R
ebGenotyping/R/ecm.R
ebGenotyping/R/my.bisec.R
ebGenotyping/R/rlogit.R
ebGenotyping/R/estep.R
ebGenotyping/MD5
ebGenotyping/DESCRIPTION
ebGenotyping/man
ebGenotyping/man/estep.Rd
ebGenotyping/man/logit.Rd
ebGenotyping/man/mstep.Rd
ebGenotyping/man/my.bisec.Rd
ebGenotyping/man/ebGenotyping-package.Rd
ebGenotyping/man/rlogit.Rd
ebGenotyping/man/ecm.Rd