aneuHMM {AneuFinder} | R Documentation

## Hidden Markov Model

### Description

The `aneuHMM` object is output of the function `findCNVs` and is basically a list with various entries. The class() attribute of this list was set to "aneuHMM". For a given hmm, the entries can be accessed with the list operators 'hmm[[]]' and 'hmm$'.

### Value

`ID` | An identifier that is used in various AneuFinder functions.
`bins` | A GRanges-class object containing the genomic bin coordinates, their read count and state classification.
`segments` | A GRanges-class object containing regions and their state classification.
`weights` | Weight for each component.
`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
`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.
`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`.

### See Also

findCNVs

[Package AneuFinder version 1.18.0 Index]