uniHMM: Univariate HMM object

Description Value See Also

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 May 2, 2020, 2:01 a.m.