RJaCGH: Reversible Jump MCMC for the Analysis of CGH Arrays

Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models. The selection of the number of states is made via their posterior probability computed by Reversible Jump Markov Chain Monte Carlo Methods. Also returns probabilistic common regions for gains/losses.

Author
Oscar Rueda <rueda.om@gmail.com> and Ramon Diaz-Uriarte <rdiaz02@gmail.com>. zlib from Jean-loup Gailly and Mark Adler; see README. Function "getHostname.System" from package R.utils by Henrik Bengtsson.
Date of publication
2015-07-10 20:15:37
Maintainer
Oscar Rueda <rueda.om@gmail.com>
License
GPL-3
Version
2.0.4
URLs

View on CRAN

Man pages

genomePlot
Plot of the genome with probabilities of alteration.
modelAveraging
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
plotQNH
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_S
Method for printing probabilistic common regions
print.summary.RJaCGH
print summary of RJaCGH fit
QNH
Transition Matrix for non-homogeneous Hidden Markov Model
relabelStates
Relabelling of hidden states to biological states of...
RJaCGH
Reversible Jump MCMC for the analysis of arrays of CGH
simulateRJaCGH
Simulate observations form a hidden Markov model with...
smoothMeans
Smoothed posterior mean
snijders
Public CGH data of Snijders
states
'states' method for RJaCGH objects
summary.RJaCGH
Summarizing RJaCGH models
trace.plot
Trace plot for 'RJaCGH' object

Files in this package

RJaCGH
RJaCGH/inst
RJaCGH/inst/doc
RJaCGH/inst/doc/RJaCGH.pdf
RJaCGH/inst/doc/Implementing_pREC_in_C.pdf
RJaCGH/inst/doc/Recurrent-regions-COBRA-reprint.pdf
RJaCGH/src
RJaCGH/src/Makevars
RJaCGH/src/nnhl.c
RJaCGH/src/Makevars.win
RJaCGH/NAMESPACE
RJaCGH/data
RJaCGH/data/snijders.RData
RJaCGH/R
RJaCGH/R/RJaCGH.R
RJaCGH/MD5
RJaCGH/DESCRIPTION
RJaCGH/Changes
RJaCGH/man
RJaCGH/man/simulateRJaCGH.Rd
RJaCGH/man/states.Rd
RJaCGH/man/pREC_A.Rd
RJaCGH/man/RJaCGH.Rd
RJaCGH/man/modelAveraging.Rd
RJaCGH/man/print.pREC_S.Rd
RJaCGH/man/plotQNH.Rd
RJaCGH/man/QNH.Rd
RJaCGH/man/relabelStates.Rd
RJaCGH/man/genomePlot.Rd
RJaCGH/man/pREC_S.Rd
RJaCGH/man/snijders.Rd
RJaCGH/man/smoothMeans.Rd
RJaCGH/man/plot.RJaCGH.Rd
RJaCGH/man/trace.plot.Rd
RJaCGH/man/print.pREC_A.Rd
RJaCGH/man/print.summary.RJaCGH.Rd
RJaCGH/man/summary.RJaCGH.Rd
RJaCGH/man/plot.pREC_S.Rd
RJaCGH/man/normal.HMM.likelihood.NH.C.Rd