GenoSet                 Create a GenoSet object
GenoSet-class           Class '"GenoSet"'
[,GenoSet,ANY-method    Subset a GenoSet
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                     Chromosome name for each feature
chrIndices              Get a matrix of first and last index of
                        features in each chromosome
chrInfo                 Get chromosome start and stop positions
chrNames                Get list of unique chromosome names
chrOrder                Order chromosome names in proper genome order
cn2lr                   Take vector or matrix of copynumber values,
                        convert to log2ratios
colMeans                Means of columns
colnames,GenoSet-method
                        Get colnames from a GenoSet
dim,GenoSet-method      Dimensions
elementLengths,GenoSet-method
                        Get elementLengths from locData slot
end,GenoSet-method      Get end of location for each feature
fixSegNAs               Fix NA runs in a Rle
gcCorrect               Correct copy number for GC content
genoPlot                Plot data along the genome
genoPos                 Get base positions of features in genome-scale
                        units
genome                  Get and set the genome universe annotation.
genome,GenoSet-method   Genome version
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 orGenoSet is in genome order
locData                 Access the feature genome position info
lr2cn                   Take vector or matrix of log2 ratios, convert
                        to copynumber
modeCenter              Center continuous data on mode
names,GenoSet-method    Get data matrix names
nrow,GRanges-method     Number of rows
pos                     Chromosome position of 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
rownames,GRanges-method
                        Get rownames from GRanges, or GenoSet
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,GenoSet-method     Print a GenoSet
start,GenoSet-method    Get start of location for each feature
subsetAssayData         Subset or re-order assayData
toGenomeOrder           Set a GRanges or GenoSet to genome order
universe,GenoSet-method
                        Get universe annotations
width,GenoSet-method    Get width of location for each feature
