findTrans.func: Funtion identifying the transitions
Description
This function identifies the start and end of the states (regions with
the constant estimated copy number).
Usage
findTrans.func(outliers, aber, statesres)
Arguments
aber
Binary matrix of the focal aberrations (generally output
of the findAber.func) Value
- trans.matrix
- Matrix with a row for each clone and column for
each sample. The starts of the states are indicated by "1" , the end
are by "2" and the focal aberrations are coded as "3"
- translen.matrix
- Matrix with a row for each clone and column for
each sample. The entries are the length of the region to which a
clone belongs. Zero length is assigned to the focal
aberrations. This output may be buggy at the moment.
Details
The transitions end is placed at the last non-focal aberration clone
of the contiguous region containing clones belonging to the same state
and transitions start is placed at the first non-focal aberration
clone of the contiguous region containing clones belonging to the same
state.
References
Application of Hidden Markov Models to the analysis of the array CGH
data, Fridlyand et.al., JMVA, 2004.