Reversible Jump MCMC for the analysis of CGH arrays.


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Documentation for package ‘RJaCGH’ version 1.2.5

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chainsSelect Select between several parallel chains ('RJaCGH' objects)
chainsSelect.RJaCGH.array Select between several parallel chains ('RJaCGH' objects)
chainsSelect.RJaCGH.Chrom Select between several parallel chains ('RJaCGH' objects)
chainsSelect.RJaCGH.genome Select between several parallel chains ('RJaCGH' objects)
collapseChain Collapse several parallel chains ('RJaCGH' objects)
collapseChain.RJaCGH.array Collapse several parallel chains ('RJaCGH' objects)
collapseChain.RJaCGH.Chrom Collapse several parallel chains ('RJaCGH' objects)
collapseChain.RJaCGH.genome Collapse several parallel chains ('RJaCGH' objects)
gelman.brooks.plot gelman-brooks plot for 'RJaCGH' objects
genome.plot Plot of the genome with probabilities of alteration.
getSequence Viterbi path from every MCMC sample
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
model.averaging Method for model averaging for RJaCGH objects.
model.averaging.RJaCGH.array Method for model averaging for RJaCGH objects.
model.averaging.RJaCGH.Chrom Method for model averaging for RJaCGH objects.
model.averaging.RJaCGH.genome 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.pREC_S.RJaCGH.array 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_A.RJaCGH.array Probabilistic Common Regions for copy number alteration.
pREC_A.RJaCGH.Chrom Probabilistic Common Regions for copy number alteration.
pREC_A.RJaCGH.genome Probabilistic Common Regions for copy number alteration.
pREC_S Subgroups of arrays that share common alterations
pREC_S.RJaCGH.array Subgroups of arrays that share common alterations
print.pREC_A Method for printing probabilistic minimal common region.
print.pREC_A.RJaCGH.array Method for printing probabilistic minimal common region.
print.pREC_A.RJaCGH.Chrom Method for printing probabilistic minimal common region.
print.pREC_A.RJaCGH.genome Method for printing probabilistic minimal common region.
print.pREC_S.RJaCGH.array Method for printing probabilistic common regions
print.summary.RJaCGH print summary of RJaCGH fit
prob.seq Joint posterior probabilities of alteration
Q.NH Transition Matrix for non-homogeneous Hidden Markov Model
relabelStates Relabelling of hidden states to biological states of alteration.
relabelStates.RJaCGH.array Relabelling of hidden states to biological states of alteration.
relabelStates.RJaCGH.Chrom Relabelling of hidden states to biological states of alteration.
relabelStates.RJaCGH.genome 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.array Smoothed posterior mean
smoothMeans.RJaCGH.Chrom Smoothed posterior mean
smoothMeans.RJaCGH.genome Smoothed posterior mean
snijders Public CGH data of Snijders
states 'states' method for RJaCGH objects
states.RJaCGH.array 'states' method for RJaCGH objects
states.RJaCGH.Chrom 'states' method for RJaCGH objects
states.RJaCGH.genome 'states' method for RJaCGH objects
summary.RJaCGH Summarizing RJaCGH models
trace.plot Trace plot for 'RJaCGH' object