BAFSet                  Create a BAFSet object
BAFSet.to.ExpressionSets
                        Make a pair of ExpressionSets from a BAFSet
CNSet                   Create a CNSet object
GenoSet                 Create a GenoSet object
asFactorMatrix          Make factor matrix from character matrix
assayDataElement        Get assayDataElement, attaching on-disk
                        resource if necessary
assayDataElement<-      Set assayDataElement, attaching on-disk
                        resource if necessary
attachAssayDataElements
                        Attach on-disk matrices into assayData
baf                     Get or Set the baf assayData slot
baf2mbaf                Calculate mBAF from BAF
bafset-class            BAFSet class
boundingIndices         Find indices of features bounding a set of
                        chromosome ranges/genes
boundingIndices2        Find indices of features bounding a set of
                        chromosome ranges/genes
boundingIndicesByChr    Find indices of features bounding a set of
                        chromosome ranges/genes, across chromosomes
chr                     Look up chromosome for each feature
chrIndices              Get a matrix of first and last index of
                        features in each chromosome
chrInfo                 Chromosome Information
chrNames                Get list of unique chromosome names
chrOrder                Order chromosome names in proper genome order
cn                      Get or Set the cn assayData slot
cnset-class             CNSet class
colMeans                Means of columns
convertToBigMatrix      Make standard matrices in a GenoSet filebacked
                        bigmatrix objects
featureNames<-          Set featureNames
gcCorrect               cgCorrect
genoPlot                Plot data along the genome
genoPos                 Convert chromosome positions to positions from
                        start of genome
genomeAxis              Label axis with base pair units
genoset-class           GenoSet class
genoset-datasets        Example GenoSet, BAFSet, and CNSet objects and
                        the data to create them.
genoset-package         GenoSet: An eSet for data with genome locations
initGenoSet             Create a GenoSet or derivative object
isGenomeOrder           Check if a GRanges, GenoSet or RangedData is in
                        genome order
loadGC                  Load local GC percentage around features
locData                 Get and set probe set info
lrr                     Get or Set the lrr assayData slot
modeCenter              Center continuous data on mode
pos                     Positions for features
rangeColMeans           Calculate column means for multiple ranges
rangeSampleMeans        Average features in ranges per sample
readGenoSet             Load a GenoSet from a RData file
relocateAssayData       Update "desc" attributes for big.matrix
                        assayDataElement to new location
runCBS                  Run CBS Segmentation
segTable                Convert Rle objects to tables of segments
segs2RangedData         Make a RangedData from segments
segs2Rle                Make Rle from segments for one sample
segs2RleDataFrame       CBS segments to probe matrix
space                   Get space factor for GenoSet
subsetAssayData         Subset assayData
toGenomeOrder           Set a GRanges, GenoSet, or RangedData to genome
                        order
universe                Get and set the genome universe annotation.
