A C D E F G I L M N P R S T V W misc
| GenoGAM-package | GenoGAM: A package providing a framework to analyse ChIP-Seq data |
| asCoordinates | IRanges to Coordinates |
| assay-method | GenoGAM class |
| assay-method | GenoGAMDataSetList |
| assay-method | GenoGAMList class |
| assays-method | GenoGAMDataSetList |
| assays-method | GenoGAMList class |
| callPeaks | Call peaks on a GenoGAM object |
| colData | GenoGAM class |
| colData-method | GenoGAM class |
| colData-method | GenoGAMDataSetList |
| colData-method | GenoGAMList class |
| colnames | GenoGAM class |
| colnames-method | GenoGAM class |
| colnames-method | GenoGAMDataSetList |
| colnames-method | GenoGAMList class |
| computeRegionSignificance | Compute significance for given regions |
| computeSignificance | computeSignificance |
| computeSizeFactors | computeSizeFactors |
| Coordinates | Coordinates class |
| Coordinates-class | Coordinates class |
| dataRange | GenoGAMDataSet |
| dataRange-method | GenoGAMDataSet |
| dataRange-method | GenoGAMDataSetList |
| design-method | GenoGAM class |
| design-method | GenoGAMDataSet |
| design-method | GenoGAMDataSetList |
| design-method | GenoGAMList class |
| design<--method | GenoGAMDataSet |
| design<--method | GenoGAMDataSetList |
| dim-method | GenoGAMDataSetList |
| dim-method | GenoGAMList class |
| dimnames | GenoGAM class |
| dimnames-method | GenoGAM class |
| dimnames-method | GenoGAMList class |
| end-method | Coordinates class |
| end<--method | Coordinates class |
| fits | GenoGAM class |
| fits-method | GenoGAM class |
| fits-method | GenoGAMList class |
| GenoGAM | GenoGAM class |
| GenoGAM | GenoGAM: A package providing a framework to analyse ChIP-Seq data |
| genogam | genogam |
| GenoGAM-class | GenoGAM class |
| GenoGAMDataSet | GenoGAMDataSet |
| GenoGAMDataSet-class | GenoGAMDataSet |
| GenoGAMDataSetList | GenoGAMDataSetList |
| GenoGAMDataSetList-class | GenoGAMDataSetList |
| GenoGAMFamily-class | GenoGAMFamily class |
| GenoGAMList | GenoGAMList class |
| GenoGAMList-class | GenoGAMList class |
| GenoGAMSettings | GenoGAMSettings |
| GenoGAMSettings-class | GenoGAMSettings |
| getChromosomes | GenoGAMDataSet |
| getChromosomes-method | GenoGAMDataSet |
| getChromosomes-method | GenoGAMDataSetList |
| getChunkSize | GenoGAMDataSet |
| getChunkSize-method | GenoGAMDataSet |
| getChunkSize-method | GenoGAMDataSetList |
| getChunkSize<- | GenoGAMDataSet |
| getChunkSize<--method | GenoGAMDataSet |
| getChunkSize<--method | GenoGAMDataSetList |
| getCoefs | GenoGAM class |
| getCoefs-method | GenoGAM class |
| getCoefs-method | GenoGAMList class |
| getCountMatrix-method | GenoGAMDataSet |
| getCountMatrix-method | GenoGAMDataSetList |
| getFamily | GenoGAM class |
| getFamily-method | GenoGAM class |
| getFamily-method | GenoGAMList class |
| getIndex | GenoGAMDataSet |
| getIndex-method | GenoGAMDataSet |
| getIndex-method | GenoGAMDataSetList |
| getKnots | GenoGAM class |
| getKnots-method | GenoGAM class |
| getKnots-method | GenoGAMList class |
| getOverhangSize | GenoGAMDataSet |
| getOverhangSize-method | GenoGAMDataSet |
| getOverhangSize-method | GenoGAMDataSetList |
| getOverhangSize<- | GenoGAMDataSet |
| getOverhangSize<--method | GenoGAMDataSet |
| getOverhangSize<--method | GenoGAMDataSetList |
| getParams | GenoGAM class |
| getParams-method | GenoGAM class |
| getParams-method | GenoGAMList class |
| getSettings | GenoGAM class |
| getSettings-method | GenoGAM class |
| getSettings-method | GenoGAMList class |
| getTileNumber | GenoGAMDataSet |
| getTileNumber-method | GenoGAMDataSet |
| getTileNumber-method | GenoGAMDataSetList |
| getTileNumber<- | GenoGAMDataSet |
| getTileNumber<--method | GenoGAMDataSet |
| getTileNumber<--method | GenoGAMDataSetList |
| getTileSize | GenoGAMDataSet |
| getTileSize-method | GenoGAMDataSet |
| getTileSize-method | GenoGAMDataSetList |
| getTileSize<- | GenoGAMDataSet |
| getTileSize<--method | GenoGAMDataSet |
| getTileSize<--method | GenoGAMDataSetList |
| IQR-method | Computing metrics |
| is.HDF5-method | GenoGAM class |
| is.HDF5-method | GenoGAMDataSet |
| is.HDF5-method | GenoGAMDataSetList |
| is.HDF5-method | GenoGAMList class |
| length-method | Coordinates class |
| length-method | GenoGAMDataSetList |
| length-method | GenoGAMList class |
| mad-method | Computing metrics |
| makeTestGenoGAM | Make an example /codeGenoGAM |
| makeTestGenoGAMDataSet | Make an example /codeGenoGAMDataSet |
| makeTestGenoGAMDataSetList | Make an example /codeGenoGAMDataSet |
| makeTestGenoGAMList | Make an example /codeGenoGAMList |
| mean-method | Computing metrics |
| median-method | Computing metrics |
| ncol-method | Coordinates class |
| nrow-method | Coordinates class |
| plotGenoGAM | The pot function for a GenoGAM object |
| pvalue-method | GenoGAM class |
| pvalue-method | GenoGAMList class |
| readData | Read Data function |
| rowRanges-method | GenoGAMDataSetList |
| rowRanges-method | GenoGAMList class |
| sd-method | Computing metrics |
| se | GenoGAM class |
| se-method | GenoGAM class |
| se-method | GenoGAMList class |
| seqlengths-method | GenoGAMDataSetList |
| seqlengths-method | GenoGAMList class |
| seqlevels-method | GenoGAMDataSetList |
| seqlevels-method | GenoGAMList class |
| seqlevelsInUse-method | GenoGAMDataSetList |
| seqlevelsInUse-method | GenoGAMList class |
| sizeFactors-method | GenoGAM class |
| sizeFactors-method | GenoGAMDataSet |
| sizeFactors-method | GenoGAMDataSetList |
| sizeFactors-method | GenoGAMList class |
| sizeFactors<--method | GenoGAMDataSet |
| sizeFactors<--method | GenoGAMDataSetList |
| start-method | Coordinates class |
| start<--method | Coordinates class |
| subset-method | Subset methods for GenoGAMDataSet |
| subset-method | Subset method for GenoGAMDataSetList |
| subset-method | Subset method for GenoGAMList |
| subsetByOverlaps-method | Subset methods for GenoGAMDataSet |
| subsetByOverlaps-method | Subset method for GenoGAMDataSetList |
| subsetByOverlaps-method | Subset method for GenoGAMList |
| Summary-method | Computing metrics |
| Summary-method | Computing metrics |
| tileSettings | GenoGAMDataSet |
| tileSettings-method | GenoGAMDataSet |
| tileSettings-method | GenoGAMDataSetList |
| var-method | Computing metrics |
| width-method | Coordinates class |
| writeToBEDFile | Write peaks to BED6+3/4 format |
| [-method | GenoGAM class |
| [-method | Subset methods for GenoGAMDataSet |
| [-method | Subset method for GenoGAMDataSetList |
| [-method | Subset method for GenoGAMList |