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