# Reversible Jump MCMC for the Analysis of CGH Arrays

## Documentation for package ‘RJaCGH’ version 2.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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