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| averageBindingValues | Set the binding values used to perform profiles and heatmaps |
| averageBindingValues<- | Set the binding values used to perform profiles and heatmaps |
| averageBindingValues<--method | Set the binding values used to perform profiles and heatmaps |
| bigWigFile | Set the path to the bigwig file |
| bigWigFile<- | Set the path to the bigwig file |
| bigWigFile<--method | Set the path to the bigwig file |
| boxplotSpike | plot boxplots of ChIP-seq experiments |
| boxplotSpike-method | plot boxplots of ChIP-seq experiments |
| ChIPSeqSpikeCore | ChIPSeqSpikeCore Reference Class |
| ChIPSeqSpikeCore-class | ChIPSeqSpikeCore Reference Class |
| ChIPSeqSpikeDataset | ChIPSeqSpikeDataset Reference Class |
| ChIPSeqSpikeDataset-class | ChIPSeqSpikeDataset Reference Class |
| ChIPSeqSpikeDatasetBoost | ChIPSeqSpikeDatasetBoost Reference Class |
| ChIPSeqSpikeDatasetBoost-class | ChIPSeqSpikeDatasetBoost Reference Class |
| ChIPSeqSpikeDatasetList | ChIPSeqSpikeDatasetList Reference Class |
| ChIPSeqSpikeDatasetList-class | ChIPSeqSpikeDatasetList Reference Class |
| ChIPSeqSpikeDatasetListBoost | ChIPSeqSpikeDatasetListBoost Reference Class |
| ChIPSeqSpikeDatasetListBoost-class | ChIPSeqSpikeDatasetListBoost Reference Class |
| count | Set the number of reads associated to an experiment |
| count<- | Set the number of reads associated to an experiment |
| count<--method | Set the number of reads associated to an experiment |
| csds | Testing data for vignette |
| datasetList | Set the list of dataset representing experiments |
| datasetList<- | Set the list of dataset representing experiments |
| datasetList<--method | Set the list of dataset representing experiments |
| estimateScalingFactors | Compute scaling factors to perform spike-in normalization |
| estimateScalingFactors-method | Compute scaling factors to perform spike-in normalization |
| exoCount | Set the number of reads associated to an experiment |
| exoCount<- | Set the number of reads associated to an experiment |
| exoCount<--method | Set the number of reads associated to an experiment |
| exogenousScalingFactor | Set the exogenous scaling factor associated to an experiment |
| exogenousScalingFactor<- | Set the exogenous scaling factor associated to an experiment |
| exogenousScalingFactor<--method | Set the exogenous scaling factor associated to an experiment |
| Experiment | Experiment Reference Class |
| Experiment-class | Experiment Reference Class |
| experimentList | Set the list of Experiment and ExperimentLoaded objects |
| experimentList<- | Set the list of Experiment and ExperimentLoaded objects |
| experimentList<--method | Set the list of Experiment and ExperimentLoaded objects |
| ExperimentLoaded | ExperimentLoaded Reference Class |
| ExperimentLoaded-class | ExperimentLoaded Reference Class |
| exportBigWigs | Export bigwig files from values contained in a boost mode object |
| exportBigWigs-method | Export bigwig files from values contained in a boost mode object |
| extractBinding | Extract binding values for graphical representations |
| extractBinding-method | Extract binding values for graphical representations |
| getAverageBindingValues | Get the average binding values associated to a dataset |
| getAverageBindingValues-method | Get the average binding values associated to a dataset |
| getBam | Get the path to an endogenous experiment bam file |
| getBam-method | Get the path to an endogenous experiment bam file |
| getBigWigFile | Get the path to an endogenous experiment bigwig file |
| getBigWigFile-method | Get the path to an endogenous experiment bigwig file |
| getCount | Get the number of reads aligned to the endogenous reference genome |
| getCount-method | Get the number of reads aligned to the endogenous reference genome |
| getDatasetList | Get the list of ChIPSeqSpike objects |
| getDatasetList-method | Get the list of ChIPSeqSpike objects |
| getExoCount | Get the number of reads aligned to the exogenous reference genome |
| getExoCount-method | Get the number of reads aligned to the exogenous reference genome |
| getExogenousBam | Get the path to an exoogenous experiment bam file |
| getExogenousBam-method | Get the path to an exoogenous experiment bam file |
| getExogenousScalingFactor | Get the exogenous scaling factor |
| getExogenousScalingFactor-method | Get the exogenous scaling factor |
| getExperimentList | Get all Experiment or ExperimentLoaded objects associated with a dataset |
| getExperimentList-method | Get all Experiment or ExperimentLoaded objects associated with a dataset |
| getExperimentListBigWigs | Get all paths to the bigwig files associated with a dataset |
| getExperimentListBigWigs-method | Get all paths to the bigwig files associated with a dataset |
| getExpName | Get the experiment name |
| getExpName-method | Get the experiment name |
| getLoadedData | Get the endogenous reference genome binding scores of an experiment |
| getLoadedData-method | Get the endogenous reference genome binding scores of an experiment |
| getMatBindingValues | Get the list of matrices of binding scores |
| getMatBindingValues-method | Get the list of matrices of binding scores |
| getRatio | Output the percentage of exogenous DNA compared to that of endogenous DNA |
| getRatio-method | Output the percentage of exogenous DNA compared to that of endogenous DNA |
| getScalingFactor | Get the endogenous scaling factor |
| getScalingFactor-method | Get the endogenous scaling factor |
| inputSubtraction | Substracts binding scores of input DNA to experiment binding scores |
| inputSubtraction-method | Substracts binding scores of input DNA to experiment binding scores |
| matBindingValues | Set the matrices of binding values |
| matBindingValues<- | Set the matrices of binding values |
| matBindingValues<--method | Set the matrices of binding values |
| plotCor | Plot the correlation between ChIP-seq experiments |
| plotCor-method | Plot the correlation between ChIP-seq experiments |
| plotHeatmaps | plot heatmaps of ChIP-seq experiments |
| plotHeatmaps-method | plot heatmaps of ChIP-seq experiments |
| plotProfile | Plots average profiles of ChIP-seq experiments |
| plotProfile-method | Plots average profiles of ChIP-seq experiments |
| plotTransform | Plots average profiles of steps of the spike-in normalization |
| plotTransform-method | Plots average profiles of steps of the spike-in normalization |
| ratio | Result of method getRatio on the complete dataset |
| result_data | Testing data for vignette |
| result_estimateScalingFactors | Testing data for vignette |
| result_extractBinding | Testing data for vignette |
| scaling | Applies different type of scaling/normalization procedures |
| scaling-method | Applies different type of scaling/normalization procedures |
| scalingFactor | Set the endogenous scaling factor associated to an experiment |
| scalingFactor<- | Set the endogenous scaling factor associated to an experiment |
| scalingFactor<--method | Set the endogenous scaling factor associated to an experiment |
| spikeDataset | spikeDataset constructors function |
| spikePipe | ChIP-seq spike-in normalization wrapper function |
| spikeSummary | Output dataset summary information |
| spikeSummary-method | Output dataset summary information |
| [[-method | ChIPSeqSpikeDataset Reference Class |
| [[-method | ChIPSeqSpikeDatasetList Reference Class |
| [[-method | ChIPSeqSpikeDatasetListBoost Reference Class |
| [[<--method | ChIPSeqSpikeDataset Reference Class |
| [[<--method | ChIPSeqSpikeDatasetList Reference Class |
| [[<--method | Experiment Reference Class |