GenoGAM                 GenoGAM: A package providing a framework to
                        analyse ChIP-Seq data
GenoGAM-class           GenoGAM class
GenoGAM-methods         GenoGAM-methods
GenoGAMDataSet          GenoGAMDataSet constructor.
GenoGAMDataSet-class    GenoGAMDataSet
GenoGAMDataSetToDataFrame
                        GenoGAMDataSet to DataFrame
GenoGAMSettings         The constructor function for GenoGAMSettings
GenoGAMSettings-class   GenoGAMSettings
GenomicTiles            GenomicTiles constructor.
GenomicTiles-class      GenomicTiles class
Summary,GenomicTiles-method
                        Computing metrics
[,GenoGAMDataSet,GRanges,ANY,ANY-method
                        Subsetting by GRanges
[[,GenomicTiles,numeric,ANY-method
                        Providing pseudo-list functionality
asDataFrame             GenomicTiles to DataFrame
callPeaks               Call peaks on a GenoGAM object
changeSettings          Check data compliance with tile settings
checkSettings           Check data compliance with tile settings
computeRegionSignificance
                        Compute significance for given regions
computeSignificance     Compute significance.
computeSizeFactors      computeSizeFactors
dataRange               The /codeGRanges of the underlying data
design,GenoGAMDataSet-method
                        Access the 'design' slot
filterData              A filter function for |codeGenoGAMDataSet
genogam                 genogam
getChromosomes          The single entries of the tile settings
getChunkIndex           Compute the index for chunks instead tiles
getCoordinates          Accessor to the /codecoordinates slot
getIndex                Accessor to the 'index' slot
getIndexCoordinates     Compute the row coordinates for a given index
getTile                 Tile extraction as a DataFrame
makeTestGenoGAM         Make an example /codeGenoGAM
makeTestGenoGAMDataSet
                        Make an example /codeGenoGAMDataSet
makeTestGenomicTiles    Make an example /codeGenomicTile
plot.GenoGAM            The pot function for a GenoGAM object
qualityCheck            A function to quality check the data
sizeFactors,GenoGAMDataSet-method
                        Access the 'sizeFactor' slot
subset,GenoGAM-method   Subset method for 'GenoGAM'
subset,GenoGAMDataSet-method
                        Subset method for 'GenoGAMDataSet'
subset,GenomicTiles-method
                        Subset method for /codeGenomciTiles
subsetByOverlaps,GenoGAM,ANY-method
                        Subset by overlaps method for 'GenoGAM'
subsetByOverlaps,GenoGAMDataSet,GRanges-method
                        Subset by overlaps method for 'GenoGAMDataSet'
subsetByOverlaps,GenomicTiles,GRanges-method
                        Subset by overlaps method for 'GenomciTiles'
tileSettings            Return tile settings
untile                  Set index to chunkIndex
view                    View the dataset
view,GenoGAM-method     View the dataset
writeToBEDFile          Write peaks to BED6+3/4 format
