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