GetSelacPhiCat: Phi rate category information under SELAC+gamma

Description Usage Arguments Details

View source: R/selac.R


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


GetSelacPhiCat(selac.obj,, aa.optim.input = NULL, = NULL, = 1)



An object of class SELAC.

Provides the path to the directory containing the gene specific fasta files of coding data.


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.

Indicates which rows to remove in the input fasta files.

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


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.