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

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

Description

Obtain posterior probilities of every state at every node

Usage

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

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")

Example output

Extracting sufficient statistics ...
Compacting sufficient statistics ...
Fitting tree model to alignment using REV ...
numpar = 11
Done.  log(likelihood) = -238483.838344 numeval=334
[1]  3  4 40
[[1]]
[1] "hg18-canFam2" "hg18-mm9"     "mm9-rn4"     

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

[[3]]
 [1] "CCTT" "CCCC" "--TT" "--T-" "--A-" "--C-" "--G-" "TTTT" "GGCC" "TGTT"
[11] "TTTC" "GGTC" "TTTG" "GG--" "CC--" "GGGG" "GAAA" "AAAA" "TTCT" "TTCC"
[21] "CTTT" "TTAA" "TATT" "AACC" "--AA" "--GG" "GCGG" "GGAA" "CCAA" "GAGG"
[31] "TTGG" "-G--" "-C--" "-A--" "GCAA" "GATT" "AATT" "CCCT" "AATC" "AACT"

                        A         C            G            T
hg18-canFam2 4.486038e-04 0.9938363 3.923823e-04 0.0053227459
hg18-mm9     6.121704e-05 0.9980161 5.356951e-05 0.0018691266
mm9-rn4      1.152963e-05 0.9995841 9.971208e-06 0.0003943768

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