uniHMM: Univariate HMM object

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

Description

The univariate HMM object is output of the function callPeaksUnivariate and is a list() with various entries. The class() attribute of this list was set to "uniHMM". For a given hmm, the entries can be accessed with the list operators 'hmm[[]]' or 'hmm$'.

Value

A list() with the following entries:

info	Experiment table for this object.
bincounts	A GRanges-class object containing the genomic bin coordinates and original binned read count values for different offsets.
bins	A GRanges-class object containing the genomic bin coordinates, their read count, (optional) posteriors and state classification.
peaks	A list() with GRanges-class containing peak coordinates for each ID in info.
weights	Weight for each component. Same as apply(hmm$posteriors,2,mean).
transitionProbs	Matrix of transition probabilities from each state (row) into each state (column).
transitionProbs.initial	Initial transitionProbs at the beginning of the Baum-Welch.
startProbs	Probabilities for the first bin. Same as hmm$posteriors[1,].
startProbs.initial	Initial startProbs at the beginning of the Baum-Welch.
distributions	Estimated parameters of the emission distributions.
distributions.initial	Distribution parameters at the beginning of the Baum-Welch.
post.cutoff	Cutoff for posterior probabilities to call peaks.
convergenceInfo	Contains information about the convergence of the Baum-Welch algorithm.
convergenceInfo$eps	Convergence threshold for the Baum-Welch.
convergenceInfo$loglik	Final loglikelihood after the last iteration.
convergenceInfo$loglik.delta	Change in loglikelihood after the last iteration (should be smaller than eps)
convergenceInfo$num.iterations	Number of iterations that the Baum-Welch needed to converge to the desired eps.
convergenceInfo$time.sec	Time in seconds that the Baum-Welch needed to converge to the desired eps.
convergenceInfo$max.mean	Value of parameter max.mean.
convergenceInfo$read.cutoff	Cutoff value for read counts.

See Also

callPeaksUnivariate, multiHMM, combinedMultiHMM

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.