BinStrain-package: BinStrain Overview
In benliemory/BinStrain: Statistical modeling for SNP based genotyping of mixed bacterial strains
Description
Description: Uses a binomial model to describe the observed alternative allele (SNP) in the targeted genomic region (or the whole genome). A well-established two step method is used to estimate the proportion of serovar strain-specific SNPs present in pure or mixed infection of genotypes. First step is a direct estimate by using the sparsity of the design matrix. Quadratic optimization method is involved in the second step. Package quadprog is needed.
Details
Package: BinStrain
Type: Package
Version: 1.0
Date: 2013-10-28
License: GPL-2
After loading your data with appropriate format, using the function "Main.function" can directly generate a text file named "betas.txt" which contains all the estimate for the parameter beta in our model.The first column of the "betas.txt" file represents the assigned consecutive numbers used to represent the reference genomes used for creating the SNP pattern file. If there are 2 or more highly similar strains with out any differentiating SNPs between them, then beta.txt file will have beta estimate for only one strain and for the rest of the similar strains will have 'NA' as estimate.
Author(s)
Sandeep J. Joseph and Ben Li
Maintainer: Sandeep J. Joseph <sandeepjoseph@emory.edu> and Ben Li <ben.li@emory.edu>
benliemory/BinStrain documentation built on May 12, 2019, 12:14 p.m.
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Description
Description: Uses a binomial model to describe the observed alternative allele (SNP) in the targeted genomic region (or the whole genome). A well-established two step method is used to estimate the proportion of serovar strain-specific SNPs present in pure or mixed infection of genotypes. First step is a direct estimate by using the sparsity of the design matrix. Quadratic optimization method is involved in the second step. Package quadprog is needed.
Details
| Package: | BinStrain |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2013-10-28 |
| License: | GPL-2 |
After loading your data with appropriate format, using the function "Main.function" can directly generate a text file named "betas.txt" which contains all the estimate for the parameter beta in our model.The first column of the "betas.txt" file represents the assigned consecutive numbers used to represent the reference genomes used for creating the SNP pattern file. If there are 2 or more highly similar strains with out any differentiating SNPs between them, then beta.txt file will have beta estimate for only one strain and for the rest of the similar strains will have 'NA' as estimate.
Author(s)
Sandeep J. Joseph and Ben Li
Maintainer: Sandeep J. Joseph <sandeepjoseph@emory.edu> and Ben Li <ben.li@emory.edu>
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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