Bayesian analysis of array CGH data

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Documentation for package ‘bayesCGH’ version 0.6

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bayesCGH-package bayesCGH - Empirical bayesian analysis of aCGH data
bayesCGH bayesCGH - Empirical bayesian analysis of aCGH data
beta Internal functions for the bayesCGH package
classifyProbes Internal functions for the bayesCGH package
ClassifySegList-class Internal functions for the bayesCGH package
compareEquivalences Bayesian comparison of proportions of chromosomal gain and loss between clinical sets.
cytobandIds Internal functions for the bayesCGH package
cytobands Internal functions for the bayesCGH package
dim,ClassifySegList-method Internal functions for the bayesCGH package
dimnames,ClassifySegList-method Internal functions for the bayesCGH package
equivalenceClasses Internal functions for the bayesCGH package
find.MCR Internal functions for the bayesCGH package
findChangePoints Internal functions for the bayesCGH package
length,ClassifySegList-method Internal functions for the bayesCGH package
logBetaOverBeta Internal functions for the bayesCGH package
logsubgamma Internal functions for the bayesCGH package
MLalphas Internal functions for the bayesCGH package
MLDirichletPriors Internal functions for the bayesCGH package
nudSegmentation Assigns each segment of each sample to either 'normal', 'up', 'down', 'amplified', or 'deleted'.
plotProportions Plots proportions of gains and losses observed in a set of array CGH data.
proportions Internal functions for the bayesCGH package
propsList Internal functions for the bayesCGH package
rdirichlet Internal functions for the bayesCGH package
rowCount Internal functions for the bayesCGH package
selectAmpsDels Selects regions with high proportions of chromosomal gains and losses.
selectRegions Selects regions with high proportions of chromosomal gains and losses.
show,ClassifySegList-method Internal functions for the bayesCGH package
summariseRegions Internal functions for the bayesCGH package
summarySelection Produce summary of selected probes.
writeSummaries Writes summaries produced by 'summariseSelection' function to file.