postprob.msa: Obtain posterior probilities of every state at every node

Description Usage Arguments Value Author(s) Examples

Description

Obtain posterior probilities of every state at every node

Usage

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postprob.msa(x, tm, every.site = FALSE)

Arguments

x

An object of type msa

tm

An object of type tm

every.site

If TRUE, return probabilities for every site rather than every site pattern (this may be very redundant and large for a large alignment with few species).

Value

An array giving the posterior probabilities of all states for every unique site pattern, or for every site if every.site is TRUE

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 <- postprob.msa(sub.msa(m, start.col=41447839, end.col=41448033,
                          refseq="hg18"), mod)
dim(x)
dimnames(x)
x[,,"CCCC"]

# now get postprobs for every site
x <- postprob.msa(sub.msa(m, start.col=41447839, end.col=41448033,
                          refseq="hg18"), mod, every.site=TRUE)
unlink("ENr334-100k.maf")


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