GetFunctionality: Calculate functionality
In bomeara/selac: Selection Models for Amino Acid and/or Codon Evolution
Description
Usage
Arguments
Details
Description
Calculates the functionality of a single gene
Usage
1
2
GetFunctionality(gene.length, aa.data, optimal.aa, alpha, beta, gamma,
gp = NULL, aa.properties = NULL)
Arguments
gene.length
Indicates the length of the gene used to calculate functionality.
aa.data
A matrix of amino acids
optimal.aa
A vector of inferred optimal amino acids.
alpha
The inferred Grantham composition paramter
beta
The inferred Grantham polarity parameter
gamma
The inferred Grantham molecular volume parameter
gp
A vector of gamma rates for calculating among site hetergeneity in functionality.
aa.properties
User-supplied amino acid distance properties. By default we assume Grantham (1974) properties.
Details
The purpose of this function is to provide the functionality of a gene based on the inferred parameters from SelAC. The functionality is often used to scale phi.
bomeara/selac documentation built on Nov. 11, 2021, 12:37 a.m.
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Description Usage Arguments Details
Description
Calculates the functionality of a single gene
Usage
1 2 | GetFunctionality(gene.length, aa.data, optimal.aa, alpha, beta, gamma,
gp = NULL, aa.properties = NULL)
|
Arguments
gene.length |
Indicates the length of the gene used to calculate functionality. |
aa.data |
A matrix of amino acids |
optimal.aa |
A vector of inferred optimal amino acids. |
alpha |
The inferred Grantham composition paramter |
beta |
The inferred Grantham polarity parameter |
gamma |
The inferred Grantham molecular volume parameter |
gp |
A vector of gamma rates for calculating among site hetergeneity in functionality. |
aa.properties |
User-supplied amino acid distance properties. By default we assume Grantham (1974) properties. |
Details
The purpose of this function is to provide the functionality of a gene based on the inferred parameters from SelAC. The functionality is often used to scale phi.
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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