col.expected.subs.msa: Obtain expected number of substitutions on each branch for...
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Author(s) Examples

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

1	col.expected.subs.msa(x, tm)

`x`	An object of type `msa`
`tm`	An object of type `tm`

An array giving the expected number of substitutions on each branch, for each distinct alignment column, for each type of substitution.

Melissa J. Hubisz and Adam Siepel

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")