Segmentation States - class

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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

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