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

1

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.

Author(s)

Melissa J. Hubisz and Adam Siepel

Examples

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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")

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