GetSelacPhiCat: Phi rate category information under SELAC+gamma

In selac: Selection Models for Amino Acid and/or Codon Evolution

Description

Provides likelihood information and best rates across sites and across genes under SELAC+gamma

Usage

GetSelacPhiCat(selac.obj, codon.data.path, aa.optim.input = NULL,
  fasta.rows.to.keep = NULL, n.cores.by.gene.by.site = 1)

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.
n.cores.by.gene.by.site	The number of cores to decidate to parallelize analyses by site WITHIN a gene. Note n.cores.by.gene*n.cores.by.gene.by.site is the total number of cores dedicated to the analysis.

Details

The purpose of this function is to determine which rate category best fits each site across genes. The output is a list object, with each list entry designating the optimal rate category across sites for that gene.

selac documentation built on July 1, 2020, 10:08 p.m.