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 |