Reversible Jump MCMC for the analysis of CGH arrays.


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Documentation for package ‘RJaCGH’ version 2.0.0

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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.Q.NH Plot transition probabilities
plot.RJaCGH 'plot' method for RJaCGH objects
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
Q.NH 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