GetSelacSiteLikelihoods: Calculate site likelihoods under SelAC
In bomeara/selac: Selection Models for Amino Acid and/or Codon Evolution
Description
Usage
Arguments
Details
Description
Calculates the likelihoods across sites and across genes under SELAC
Usage
1
2
GetSelacSiteLikelihoods(selac.obj, codon.data.path,
aa.optim.input = NULL, fasta.rows.to.keep = NULL)
Arguments
selac.obj
An object of class SELAC.
codon.data.path
Provides the path to the directory containing the gene specific fasta files of coding data.
aa.optim.input
A list of optimal amino acids with each list element designating a character vector for each gene. The optimal amino acids be the MLE from a selac run (default) or a list of user defined optimal A.A.
fasta.rows.to.keep
Indicates which rows to remove in the input fasta files.
Details
The purpose of this function is to provide the site likelihoods across genes. It is also flexible in that it allows different hypotheses about optimal acids across genes and/or site. The output is a list object, with each list entry designating 1) the tot.likelihood for that gene, and 2) the site likelihoods for that gene.
bomeara/selac documentation built on Nov. 11, 2021, 12:37 a.m.
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.
Description Usage Arguments Details
Description
Calculates the likelihoods across sites and across genes under SELAC
Usage
1 2 | GetSelacSiteLikelihoods(selac.obj, codon.data.path,
aa.optim.input = NULL, fasta.rows.to.keep = NULL)
|
Arguments
selac.obj |
An object of class SELAC. |
codon.data.path |
Provides the path to the directory containing the gene specific fasta files of coding data. |
aa.optim.input |
A list of optimal amino acids with each list element designating a character vector for each gene. The optimal amino acids be the MLE from a selac run (default) or a list of user defined optimal A.A. |
fasta.rows.to.keep |
Indicates which rows to remove in the input fasta files. |
Details
The purpose of this function is to provide the site likelihoods across genes. It is also flexible in that it allows different hypotheses about optimal acids across genes and/or site. The output is a list object, with each list entry designating 1) the tot.likelihood for that gene, and 2) the site likelihoods for that gene.
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.