rphast (version 1.6.9)

read.hmm: Read an HMM object from a file

Description

This function uses phast's internal hmm format, which is quite simple. See write.hmm or file used in example below for exaples of hmm format.

Usage

read.hmm(filename)

Arguments

filename

The file to read

Value

An hmm object

Examples

# NOT RUN {
exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
file <- "coding.hmm"
unzip(exampleArchive, file)
# this is a 5-state hmm with states representing
# intergenic, intron, first, second, and third codon positions.
h <- read.hmm(file)
h
unlink(file)
# }