RJaCGH: Reversible Jump MCMC for the Analysis of CGH Arrays
Version 2.0.4

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.

AuthorOscar 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.
Bioconductor views DNACopyNumber Microarray
Date of publication2015-07-10 20:15:37
MaintainerOscar Rueda <rueda.om@gmail.com>
LicenseGPL-3
Version2.0.4
URL http://www.r-project.org
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RJaCGH")

Popular 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.RJaCGH: 'plot' method for RJaCGH objects
relabelStates: Relabelling of hidden states to biological states of...
simulateRJaCGH: Simulate observations form a hidden Markov model with...
states: 'states' method for RJaCGH objects
See all...

All man pages Function index File listing

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

Functions

MetropolisSweep.C Source code
QNH Man page Source code
RJMCMC.NH.HMM.Metropolis Source code
RJaCGH Man page Source code
akaike Source code
check.no.float Source code
createRegionsList Source code
f2tmp Source code
genomePlot Man page Source code
get.jump Source code
get.viterbi.seq2 Source code
getHostname.System Source code
getStretchedStateProbs Source code
gm00143 Man page
gm01524 Man page
gm01535 Man page
gm01750 Man page
gm02948 Man page
gm03134 Man page
gm03563 Man page
gm03576 Man page
gm04435 Man page
gm05296 Man page
gm07081 Man page
gm07408 Man page
gm10315 Man page
gm13031 Man page
gm13330 Man page
hidden.states Source code
internal.plot.obs.pred Source code
modelAveraging Man page Source code
modelAveraging.RJaCGH Man page Source code
modelAveraging.RJaCGH.Chrom Source code
modelAveraging.RJaCGH.Genome Source code
modelAveraging.iRJaCGH Source code
normal.HMM.likelihood.NH.C Man page Source code
normal.HMM.likelihood.NH.filter Source code
pREC Source code
pREC_A Man page Source code
pREC_A.RJaCGH Man page
pREC_A.RJaCGH.Chrom Man page
pREC_A.RJaCGH.array Man page
pREC_A.RJaCGH.genome Man page
pREC_S Man page Source code
pREC_S.RJaCGH Man page
pREC_S.RJaCGH.array Man page
pREC_S.RJaCGH.array.Chrom Man page
pREC_S.RJaCGH.array.genome Man page
plot.RJaCGH Man page Source code
plot.RJaCGH.Chrom Source code
plot.RJaCGH.Genome Source code
plot.pREC_S Man page Source code
plotQNH Man page Source code
print.pREC_A Man page Source code
print.pREC_A.Chromosomes Man page Source code
print.pREC_A.none Man page Source code
print.pREC_S Man page Source code
print.pREC_S.Chromosomes Man page Source code
print.pREC_S.none Man page Source code
print.summary.RJaCGH Man page Source code
print.summary.RJaCGH.Chrom Man page Source code
print.summary.RJaCGH.Genome Man page Source code
print.summary.iRJaCGH Source code
readRO2 Source code
relabel.core Source code
relabelStates Man page Source code
relabelStates.RJaCGH Man page Source code
relabelStates.RJaCGH.Chrom Source code
relabelStates.RJaCGH.Genome Source code
relabelStates.iRJaCGH Source code
scale.bound.Dist Source code
simulateRJaCGH Man page Source code
smoothMeans Man page Source code
smoothMeans.RJaCGH Man page Source code
smoothMeans.RJaCGH.Chrom Source code
smoothMeans.RJaCGH.Genome Source code
smoothMeans.iRJaCGH Source code
snijders Man page
states Man page Source code
states.RJaCGH Man page Source code
states.RJaCGH.Chrom Source code
states.RJaCGH.Genome Source code
states.iRJaCGH Source code
summary.RJaCGH Man page Source code
summary.RJaCGH.Chrom Source code
summary.RJaCGH.Genome Source code
summary.iRJaCGH Source code
tempdir.RJaCGH Source code
tempdir2 Source code
tempfile00 Source code
tempfile2 Source code
tempfile3 Source code
the.time.with.ms Source code
trace.plot Man page Source code
writeRO2 Source code

Files

inst
inst/doc
inst/doc/RJaCGH.pdf
inst/doc/Implementing_pREC_in_C.pdf
inst/doc/Recurrent-regions-COBRA-reprint.pdf
src
src/Makevars
src/nnhl.c
src/Makevars.win
NAMESPACE
data
data/snijders.RData
R
R/RJaCGH.R
MD5
DESCRIPTION
Changes
man
man/simulateRJaCGH.Rd
man/states.Rd
man/pREC_A.Rd
man/RJaCGH.Rd
man/modelAveraging.Rd
man/print.pREC_S.Rd
man/plotQNH.Rd
man/QNH.Rd
man/relabelStates.Rd
man/genomePlot.Rd
man/pREC_S.Rd
man/snijders.Rd
man/smoothMeans.Rd
man/plot.RJaCGH.Rd
man/trace.plot.Rd
man/print.pREC_A.Rd
man/print.summary.RJaCGH.Rd
man/summary.RJaCGH.Rd
man/plot.pREC_S.Rd
man/normal.HMM.likelihood.NH.C.Rd
RJaCGH documentation built on May 20, 2017, 4:45 a.m.

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