getPosterior: Calculate posterior state distribution.

In STAN: The Genomic STate ANnotation Package

Description

The function calculates posterior state probabilities for one or more observation sequence.

Usage

getPosterior(hmm, obs=list(), emissionProbs=list(), dirFlags=list(), verbose=FALSE, nCores=1, sizeFactors=matrix(1, nrow=length(obs), ncol=ncol(obs[[1]])))

Arguments

hmm	The Hidden Markov Model.
obs	The observations. A list of one or more entries containing the observation matrix (numeric) for the samples (e.g. chromosomes).
emissionProbs	List of precalculated emission probabilities of emission function is of type 'null'.
dirFlags	The flag sequence is needed when a bdHMM is fitted on undirected data (e.g.) ChIP only. It is a list of character vectors indication for each position its knwon directionality. U allows all states. F allows undirected states and states in forward direction. R allows undirected states and states in reverse direction.
verbose	logical for printing algorithm status or not.
nCores	Number of cores to use for computations.
sizeFactors	Library size factors for Emissions PoissonLogNormal or NegativeBinomial as a length(obs) x ncol(obs[[1]]) matrix.

Value

A list containing for the observation sequences the posterior state (col) distribution at each position (row).

Examples

data(example)
hmm_ex = initHMM(observations, nStates=3, method="Gaussian") 
hmm_fitted = fitHMM(observations, hmm_ex)
posterior = getPosterior(hmm_fitted, observations)

STAN documentation built on Nov. 8, 2020, 11:11 p.m.