transitionFrequencies {chromstaR} | R Documentation

## Transition frequencies of combinatorial states

### Description

Get a table of transition frequencies between combinatorial states of different `multiHMM`s.

### Usage

    transitionFrequencies(
      multi.hmms = NULL,
      combined.hmm = NULL,
      zero.states = "[]",
      combstates = NULL
    )

### Arguments

`multi.hmms` | A named list with `multiHMM` objects or a vector with filenames that contain such objects.
`combined.hmm` | A `combinedMultiHMM` object. If specified, `multi.hmms` is ignored.
`zero.states` | The string(s) which identifies the zero.states.
`combstates` | Alternative input instead of `multi.hmms`: A named list of combinatorial state vectors instead of HMMs. Names must be of the form "combination.X", where X is an arbitrary string. If this is specified, `multi.hmms` and `combined.hmm` will be ignored.

### Value

A data.frame with transition frequencies.

### Author(s)

Aaron Taudt

### Examples

    ## Get an example combinedMultiHMM
    file <- system.file("data","combined_mode-differential.RData",
                        package="chromstaR")
    model <- get(load(file))
    freqs <- transitionFrequencies(combined.hmm=model)
    freqs$table

[Package chromstaR version 1.14.1 Index]