rphast (version 1.6.9)

expected.subs.msa: Obtain expected number of substitutions on each branch and site

Description

Obtain expected number of substitutions on each branch and site

Usage

expected.subs.msa(x, tm)

Arguments

x

An object of type msa

tm

An object of type tm

Value

An array giving the expected number of substitutions on each branch at each unique site pattern, summed across all types of substitutions.

Examples

# NOT RUN {
exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
unzip(exampleArchive, "ENr334-100k.maf")
m <- read.msa("ENr334-100k.maf")
mod <- phyloFit(m, tree="((hg18,(mm9,rn4)),canFam2)")
x <- expected.subs.msa(sub.msa(m, start.col=41447839, end.col=41448033, refseq="hg18"), mod)
dim(x)
dimnames(x)
x[,"CCCC"]
x["mm9-rn4",]
unlink("ENr334-100k.maf")
# }