uniHMM {chromstaR} | R Documentation

## Univariate HMM object

### 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`

[Package chromstaR version 1.10.0 Index]