mod.backgd.tm: Adjust tree model background frequencies while maintaining...

Description Usage Arguments Note Author(s) Examples

View source: R/treeModel.R

Description

Adjust tree model background frequencies while maintaining reversibility

Usage

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mod.backgd.tm(tm, new.backgd = NULL, gc = NULL)

Arguments

tm

An object of type tm

new.backgd

A numeric vector of length 4 giving the background frequencies of A,C,G,T

gc

(Alternative to new.backgd) A numeric value giving the GC content, which is used to calculate new background frequencies. Assumes freq(C)==freq(G)==gc/2, and freq(A)==freq(T)==(1-gc)/2

Note

Currently only works with models of order 0, without lineage- specific models, and which use the default alphabet "ACGT".

Author(s)

Melissa J. Hubisz and Adam Siepel

Examples

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exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
filename <- "rev.mod"
unzip(exampleArchive, filename)
tm <- read.tm(filename)

# change background frequencies to new value, adjusting rate matrix
mod.backgd.tm(tm, c(0.25, 0.25, 0.25, 0.25))

# change background frequencies so that GC content is 0.6
mod.backgd.tm(tm, gc=0.6)

unlink(filename)

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