transitionFrequencies: Transition frequencies of combinatorial states

In ataudt/chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Description

Get a table of transition frequencies between combinatorial states of different multiHMMs.

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

ataudt/chromstaR documentation built on Dec. 26, 2021, 12:07 a.m.