Q.NH                    Transition Matrix for non-homogeneous Hidden
                        Markov Model
RJaCGH                  Reversible Jump MCMC for the analysis of arrays
                        of CGH
genomePlot              Plot of the genome with probabilities of
                        alteration.
modelAveraging          Method for model averaging for RJaCGH objects.
normal.HMM.likelihood.NH.C
                        Likelihood for non-homogeneous hidden Markov
                        model
pREC_A                  Probabilistic Common Regions for copy number
                        alteration.
pREC_S                  Subgroups of arrays that share common
                        alterations
plot.Q.NH               Plot transition probabilities
plot.RJaCGH             'plot' method for RJaCGH objects
plot.pREC_S             Plot number of probes shared by pairs of arrays
print.pREC_A            Method for printing probabilistic common
                        region.
print.pREC_S            Method for printing probabilistic common
                        regions
print.summary.RJaCGH    print summary of RJaCGH fit
relabelStates           Relabelling of hidden states to biological
                        states of alteration.
simulateRJaCGH          Simulate observations form a hidden Markov
                        model with non-homogeneous transition
                        probabilities.
smoothMeans             Smoothed posterior mean
snijders                Public CGH data of Snijders
states                  'states' method for RJaCGH objects
summary.RJaCGH          Summarizing RJaCGH models
trace.plot              Trace plot for 'RJaCGH' object
