GetSelacPhiCat: Phi rate category information under SELAC+gamma

Description Usage Arguments Details

View source: R/selac.R

Description

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

Usage

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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.


bomeara/selac documentation built on Jan. 11, 2020, 11:12 a.m.