asDataFrame | GenomicTiles to DataFrame |
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 |
computeSignificance | Compute significance. |
computeSizeFactors | computeSizeFactors |
dataRange | The /codeGRanges of the underlying data |
dataRange-method | The /codeGRanges of the underlying data |
design-method | Access the 'design' slot |
design<--method | Access the 'design' slot |
GenoGAM | GenoGAM: A package providing a framework to analyse ChIP-Seq data |
genogam | genogam |
GenoGAM-class | GenoGAM class |
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 | Accessor to 'fits' slot |
getFits-method | Accessor to 'fits' slot |
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 |
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 |
[-method | Providing pseudo-list functionality |
[[-method | Providing pseudo-list functionality |