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 |