BAFSet                  Create a BAFSet object
BAFSet-class            Class '"BAFSet"'
BAFSet.to.ExpressionSets
                        Make a pair of ExpressionSets from a BAFSet
CNSet                   Create a CNSet object
CNSet-class             Class '"CNSet"'
GenoSet                 Create a GenoSet object
GenoSet-class           Class '"GenoSet"'
baf                     Get baf data
baf2mbaf                Calculate mBAF from BAF
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
bounds2Rle              Convert bounding indices into a Rle
calcGC                  Calculate GC Percentage in windows
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
cn2lr                   Take vector or matrix of copynumber values,
                        convert to log2ratios Utility function for
                        converting copynumber units (2 is normal) to
                        log2ratio units (two is normal)
colMeans                Means of columns
colnames                Get colnames from a GenoSet
featureNames            Get rownames from RangedData, GRanges, or
                        GenoSet
fixSegNAs               Fix NA runs in a Rle
gcCorrect               Correct copy number for GC content
genoPlot                Plot data along the genome
genoPos                 Convert chromosome positions to positions from
                        start of genome
genome                  Get and set the genome universe annotation.
genomeAxis              Label axis with base pair units
genoset-datasets        Example GenoSet, BAFSet, and CNSet objects and
                        the data to create them.
genoset-defunct         Defunct genoset features
genoset-deprecated      Deprecated genoset features
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
locData                 Access the feature genome position info
lr2cn                   Take vector or matrix of log2 ratios, convert
                        to copynumber Utility function for converting
                        log2ratio units (zero is normal) to copynumber
                        units (two is normal)
lrr                     Get lrr data
modeCenter              Center continuous data on mode
pos                     Positions for features
rangeColMeans           Calculate column means for multiple ranges
rangeSampleMeans        Average features in ranges per sample
rangeSegMeanLength      Get segment widths
readGenoSet             Load a GenoSet from a RData file
runCBS                  Run CBS Segmentation
segPairTable            Convert Rle objects to tables of segments
segTable                Convert Rle objects to tables of segments
segs2Granges            GRanges from segment table
segs2RangedData         Make a RangedData from segments
segs2Rle                Make Rle from segments for one sample
segs2RleDataFrame       CBS segments to probe matrix
show                    Show a GenoSet
start                   Get start of location for each feature
subsetAssayData         Subset assayData
toGenomeOrder           Set a GRanges, GenoSet, or RangedData to genome
                        order
