bgc.nucleotide.tests: Do maximum likelihood analysis for gBGC and selection using...

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

Do maximum likelihood analysis for gBGC and selection using nucleotide model

Usage

bgc.nucleotide.tests(align, neutralMod, branch, sel.limits = c(-200, 200),
  bgc.limits = c(0, 200))

Arguments

align	A nucleotide alignment of type msa
neutralMod	A model of neutral evolution of type tm. Should be a nucleotide (4x4) model.
branch	A character string giving the name of a branch from neutralMod$tree where lineage-specific selection/gBGC
sel.limits	Numeric vector of length 2 giving lower and upper limits for selection parameter.
bgc.limits	Numeric vector of length 2 giving lower and upper limits for gBGC parameter B

Value

A data.frame with four rows. Each row represents one of the models "null", "sel", "bgc", and "sel+bgc". All models have a global selection coefficient; the sel and sel+bgc models have a lineage-specific selection coefficient as well, and the bgc and sel+bgc models have a lineage-specific gBGC parameter. The likelihoods and parameter estimates for each model are returned in the data frame.

Author(s)

Melissa J. Hubisz

rphast documentation built on May 1, 2019, 9:26 p.m.