Reversible Jump MCMC for the analysis of CGH arrays.


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Documentation for package `RJaCGH' version 1.0.2

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chainsSelect Select between several parallel chains ('RJaCGH' objects)
chainsSelect.RJaCGH.array 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.
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.Q.NH Plot transition probabilities
plot.RJaCGH 'plot' method for RJaCGH objects
pMCR Probabilistic Minimal Common Regions for copy number alteration.
pMCR.RJaCGH.array Probabilistic Minimal Common Regions for copy number alteration.
pMCR.RJaCGH.Chrom Probabilistic Minimal Common Regions for copy number alteration.
pMCR.RJaCGH.genome Probabilistic Minimal Common Regions for copy number alteration.
print.pMCR.RJaCGH Method for printing probabilistic minimal common region.
print.pMCR.RJaCGH.array.Chrom Method for printing probabilistic minimal common region.
print.pMCR.RJaCGH.array.genome Method for printing probabilistic minimal common region.
print.pMCR.RJaCGH.Chrom Method for printing probabilistic minimal common region.
print.pMCR.RJaCGH.genome Method for printing probabilistic minimal common region.
Q.NH Transition Matrix for non-homogeneous Hidden Markov Model
RJaCGH Reversible Jump MCMC for the analysis of arrays of CGH
simulateRJaCGH Simulate observations form a hidden Markov model with non-homogeneous transition probabilities.
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