setup.branch.site.tm: Set up a tree model for branch site selection analysis

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

Description

Set up a tree model for branch site selection analysis

Usage

setup.branch.site.tm(mod, foreground, bgc = FALSE, altModel = TRUE,
  init.sel.neg = 0, init.sel.pos = 0, init.bgc = 0, init.weights = NULL)

Arguments

mod	an object of type tm
foreground	a character string giving a tree branch name or label identifying foreground branches
bgc	If TRUE, then use 8 categories of sites; four with bgc in the foreground and four without.
altModel	If TRUE, then optimize the foreground positive selection parameter (constrained > 0). Otherwise hold constant at 0.
init.sel.neg	Initial value for negative selection parameter
init.sel.pos	Initial value for positive selection paramter
init.bgc	Initial value for bgc parameter (Ignored if bgc==FALSE)
init.weights	Numeric vector of length three giving the initial weight parameters. The first two values determine the relative frequencies of negatively, neutral, and positively selected sites. The last parameter determines the frequency of sites affected by bgc, and is ignored if bgc==FALSE. All values should be >= 0.

Value

An object of type tm which can be used as the init.mod argument to phyloFit to perform the branch-site test.

Author(s)

Melissa J. Hubisz

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