# findTrans.func

0th

Percentile

##### Funtion identifying the transitions

This function identifies the start and end of the states (regions with the constant estimated copy number).

Keywords
models
##### Usage
findTrans.func(outliers, aber, statesres)
##### Arguments
outliers
Binary matrix of the outliers (generally output of the findOutliers.func)
aber
Binary matrix of the focal aberrations (generally output of the findAber.func)
statesres
The states output of the hmm.run.func
##### 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.

##### 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.

##### References

Application of Hidden Markov Models to the analysis of the array CGH data, Fridlyand et.al., JMVA, 2004.

aCGH