findTrans.func {aCGH} | R Documentation |
This function identifies the start and end of the states (regions with the constant estimated copy number).
findTrans.func(outliers = res1$outliers, aber = res2$aber, statesres = states.bic)
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 |
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.
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. |
Jane Fridlyand
Application of Hidden Markov Models to the analysis of the array CGH data, Fridlyand et.al., JMVA, 2004.