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| genomePlot | Plot of the genome with probabilities of alteration. |
| gm00143 | Public CGH data of Snijders |
| gm01524 | Public CGH data of Snijders |
| gm01535 | Public CGH data of Snijders |
| gm01750 | Public CGH data of Snijders |
| gm02948 | Public CGH data of Snijders |
| gm03134 | Public CGH data of Snijders |
| gm03563 | Public CGH data of Snijders |
| gm03576 | Public CGH data of Snijders |
| gm04435 | Public CGH data of Snijders |
| gm05296 | Public CGH data of Snijders |
| gm07081 | Public CGH data of Snijders |
| gm07408 | Public CGH data of Snijders |
| gm10315 | Public CGH data of Snijders |
| gm13031 | Public CGH data of Snijders |
| gm13330 | Public CGH data of Snijders |
| modelAveraging | Method for model averaging for RJaCGH objects. |
| modelAveraging.RJaCGH | Method for model averaging for RJaCGH objects. |
| normal.HMM.likelihood.NH.C | Likelihood for non-homogeneous hidden Markov model |
| plot.pREC_S | Plot number of probes shared by pairs of arrays |
| plot.RJaCGH | 'plot' method for RJaCGH objects |
| plotQNH | Plot transition probabilities |
| pREC_A | Probabilistic Common Regions for copy number alteration. |
| pREC_S | Subgroups of arrays that share common alterations |
| print.pREC_A | Method for printing probabilistic common region. |
| print.pREC_A.Chromosomes | Method for printing probabilistic common region. |
| print.pREC_A.none | Method for printing probabilistic common region. |
| print.pREC_S | Method for printing probabilistic common regions |
| print.pREC_S.Chromosomes | Method for printing probabilistic common regions |
| print.pREC_S.none | Method for printing probabilistic common regions |
| print.summary.RJaCGH | print summary of RJaCGH fit |
| print.summary.RJaCGH.Chrom | print summary of RJaCGH fit |
| print.summary.RJaCGH.Genome | print summary of RJaCGH fit |
| QNH | Transition Matrix for non-homogeneous Hidden Markov Model |
| relabelStates | Relabelling of hidden states to biological states of alteration. |
| relabelStates.RJaCGH | Relabelling of hidden states to biological states of alteration. |
| RJaCGH | Reversible Jump MCMC for the analysis of arrays of CGH |
| simulateRJaCGH | Simulate observations form a hidden Markov model with non-homogeneous transition probabilities. |
| smoothMeans | Smoothed posterior mean |
| smoothMeans.RJaCGH | Smoothed posterior mean |
| snijders | Public CGH data of Snijders |
| states | 'states' method for RJaCGH objects |
| states.RJaCGH | 'states' method for RJaCGH objects |
| summary.RJaCGH | Summarizing RJaCGH models |
| trace.plot | Trace plot for 'RJaCGH' object |