rphast (version 1.6.9)

col.expected.subs.msa: Obtain expected number of substitutions on each branch for each site pattern and each substitution type

Description

Obtain expected number of substitutions on each branch for each site pattern and each substitution type

Usage

col.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, for each distinct alignment column, for each type of substitution.

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 <- col.expected.subs.msa(sub.msa(m, start.col=41447839, end.col=41448033, refseq="hg18"), mod)
dim(x)
dimnames(x)
x["mm9-rn4","CCTT",,]
unlink("ENr334-100k.maf")
# }