SegList-class {snapCGH} | R Documentation

## Segmentation States - class

### Description

A list based class for storing the results of a segmentation algorithm. They are generally created by running one of the following functions `runHomHMM`, `runGLAD` or `runDNAcopy` on an `MAList object`.

### Slots/List Components

Objects should contain the following list components:

`pred`: | Predicted value of the state.
`disp`: | Dispersion.
`obs`: | Observed value.
`state`: | Numeric value.
`nstates.hmm`: | The number of states per chromosome. Each row represents a chromosome and each column is an array.
`genes`: | data.frame that contains the chromosome and position on the chromosome for each clone. Used for plotting functions.

Optional:

`rpred`: | Smoothed value for the clone.
`prob`: | Probability of the clone being in the assigned state.

### Methods

`SegLists` can be subsetted and combined. They also return dimensions so functions such as `dim`, `nrow` and `ncol` are also defined. `SegList` inherits the `show` method from the Limma class `LargeDataObject`. This means that the `SegList` will print in a relatively compact way.

### Author(s)

Mike Smith

[Package snapCGH version 1.2.0 Index]