total.expected.subs.msa: Obtain expected number of substitutions of each type on each...

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

Obtain expected number of substitutions of each type on each branch

Usage

total.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 type of substitution.

Author(s)

Melissa J. Hubisz and Adam Siepel

Examples

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

Example output

Extracting sufficient statistics ...
Compacting sufficient statistics ...
Fitting tree model to alignment using REV ...
numpar = 11
Done.  log(likelihood) = -238483.838367 numeval=332
[1] 6 4 4
[[1]]
[1] "hg18-mm9" "hg18"     "mm9-rn4"  "mm9"      "rn4"      "canFam2" 

[[2]]
[1] "from.A" "from.C" "from.G" "from.T"

[[3]]
[1] "to.A" "to.C" "to.G" "to.T"

            to.A      to.C       to.G      to.T
from.A 38.813358  3.487672  1.0370545  2.701512
from.C  2.690418 74.424677  0.4165913  6.435992
from.G  5.246924  3.126923 39.9781609  2.109085
from.T  2.328609  2.650553  1.2303032 45.322169

rphast documentation built on May 1, 2019, 9:26 p.m.