| SegList-class {snapCGH} | R Documentation |
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.
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. |
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.
Other functions which operate on SegList objects include:
plotSegmentationStates
Mike Smith