Funtion identifying the transitions
This function identifies the start and end of the states (regions with the constant estimated copy number).
findTrans.func(outliers, aber, statesres)
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.
- 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"
- 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.
Application of Hidden Markov Models to the analysis of the array CGH data, Fridlyand et.al., JMVA, 2004.