Description Usage Arguments Note Author(s) Examples
Adjust tree model background frequencies while maintaining reversibility
1 | mod.backgd.tm(tm, new.backgd = NULL, gc = NULL)
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tm |
An object of type |
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 |
Currently only works with models of order 0, without lineage- specific models, and which use the default alphabet "ACGT".
Melissa J. Hubisz and Adam Siepel
1 2 3 4 5 6 7 8 9 10 11 12 | 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)
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