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...
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
                        chromsome ranges/genes...
boundingIndices2        Find indices of features bounding a set of
                        chromsome ranges/genes...
chr-methods             Look up chromosome for each feature
chrIndices-methods      Get a matrix of first and last index of
                        features in each chromosome...
chrInfo                 Chromosome Information
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...
gcCorrect               cgCorrect
genoPlot                genoPlot,-method
genoPos-methods         Convert chromosome positions to positions from
                        start of genome
genomeAxis              Label axis with base pair units
genoset                 Example GenoSet, BAFSet, and CNSet objects and
                        the data to create them.
genoset-class           GenoSet class
initGenoSet             Create a GenoSet or derivative object...
isGenomeOrder           Check if a RangedData or GenoSet is in genome
                        order...
locData                 Get and set probe set info
lrr                     Get or Set the lrr assayData slot...
modeCenter              Center continuous data on mode...
orderedChrs             Get chromosome names in genome order...
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...
runCBS                  Run CBS Segmentation
segTable-methods        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,-method           Get space factor for GenoSet...
subsetAssayData         Subset assayData
toGenomeOrder,RangedData-method
                        Get indices to set a RangedData or GenoSet to
                        genome order...
uniqueChrs              Get list of unique chromosome names...
universe                Get and set the genome universe annotation.
