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ebGenotyping  

Genotyping and SNP Detection using Next Generation Sequencing Data
View on CRAN: Click here


Download and install ebGenotyping package within the R console
Install from CRAN:
install.packages("ebGenotyping")

Install from Github:
library("remotes")
install_github("cran/ebGenotyping")

Install by package version:
library("remotes")
install_version("ebGenotyping", "2.0.1")



Attach the package and use:
library("ebGenotyping")
Maintained by
Gongyi Huang
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-05-05
Latest Update: 2016-04-13
Description:
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.
How to cite:
Gongyi Huang (2015). ebGenotyping: Genotyping and SNP Detection using Next Generation Sequencing Data. R package version 2.0.1, https://cran.r-project.org/web/packages/ebGenotyping. Accessed 21 Nov. 2024.
Previous versions and publish date:
1.0 (2015-05-05 16:14)
Other packages that cited ebGenotyping R package
View ebGenotyping citation profile
Other R packages that ebGenotyping depends, imports, suggests or enhances
Complete documentation for ebGenotyping
Functions, R codes and Examples using the ebGenotyping R package
Some associated functions: ebGenotyping-package . ecm . estep . logit . mstep . my.bisec . rlogit . 
Some associated R codes: ecm.R . estep.R . logit.R . mstep.R . my.bisec.R . rlogit.R .  Full ebGenotyping package functions and examples
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