multiHMM {chromstaR} | R Documentation

## Multivariate HMM object

### Description

The multivariate HMM object is output of the function `callPeaksMultivariate` and is a `list()` with various entries. The `class()` attribute of this list was set to "multiHMM". 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.
`segments` | Same as `bins`, but consecutive bins with the same state are collapsed into segments.
`peaks` | A `list()` with `GRanges-class` containing peak coordinates for each ID in `info`.
`mapping` | A named vector giving the mapping from decimal combinatorial states to human readable combinations.
`weights` | Weight for each component. Same as `apply(hmm$posteriors,2,mean)`.
`weights.univariate` | Weights of the univariate HMMs.
`transitionProbs` | Matrix of transition probabilities from each state (row) into each state (column).
`transitionProbs.initial` | Initial `transitionProbs` at the beginning of the Baum-Welch.
`startProbs` | Probabilities for the first bin. Same as `hmm$posteriors[1,]`.
`startProbs.initial` | Initial `startProbs` at the beginning of the Baum-Welch.
`distributions` | Emission distributions used for this model.
`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`.
`correlation.matrix` | Correlation matrix of transformed reads.

### See Also

`callPeaksMultivariate`, `uniHMM`, `combinedMultiHMM`

### Examples

    ## Get an example multiHMM
    file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData",
                        package="chromstaR")
    model <- get(load(file))

[Package chromstaR version 1.8.1 Index]