Man pages for ChIPSeqSpike
ChIP-Seq data scaling according to spike-in control

averageBindingValuesSet the binding values used to perform profiles and heatmaps
bigWigFileSet the path to the bigwig file
boxplotSpikeplot boxplots of ChIP-seq experiments
ChIPSeqSpikeCoreChIPSeqSpikeCore Reference Class
ChIPSeqSpikeDatasetBoost-classChIPSeqSpikeDatasetBoost Reference Class
ChIPSeqSpikeDataset-classChIPSeqSpikeDataset Reference Class
ChIPSeqSpikeDatasetListBoost-classChIPSeqSpikeDatasetListBoost Reference Class
ChIPSeqSpikeDatasetList-classChIPSeqSpikeDatasetList Reference Class
countSet the number of reads associated to an experiment
datasetListSet the list of dataset representing experiments
estimateScalingFactorsCompute scaling factors to perform spike-in normalization
exoCountSet the number of reads associated to an experiment
exogenousScalingFactorSet the exogenous scaling factor associated to an experiment
Experiment-classExperiment Reference Class
experimentListSet the list of Experiment and ExperimentLoaded objects
ExperimentLoaded-classExperimentLoaded Reference Class
exportBigWigsExport bigwig files from values contained in a boost mode...
extractBindingExtract binding values for graphical representations
getAverageBindingValuesGet the average binding values associated to a dataset
getBamGet the path to an endogenous experiment bam file
getBigWigFileGet the path to an endogenous experiment bigwig file
getCountGet the number of reads aligned to the endogenous reference...
getDatasetListGet the list of ChIPSeqSpike objects
getExoCountGet the number of reads aligned to the exogenous reference...
getExogenousBamGet the path to an exoogenous experiment bam file
getExogenousScalingFactorGet the exogenous scaling factor
getExperimentListGet all Experiment or ExperimentLoaded objects associated...
getExperimentListBigWigsGet all paths to the bigwig files associated with a dataset
getExpNameGet the experiment name
getLoadedDataGet the endogenous reference genome binding scores of an...
getMatBindingValuesGet the list of matrices of binding scores
getRatioOutput the percentage of exogenous DNA compared to that of...
getScalingFactorGet the endogenous scaling factor
inputSubtractionSubstracts binding scores of input DNA to experiment binding...
matBindingValuesSet the matrices of binding values
plotCorPlot the correlation between ChIP-seq experiments
plotHeatmapsplot heatmaps of ChIP-seq experiments
plotProfilePlots average profiles of ChIP-seq experiments
plotTransformPlots average profiles of steps of the spike-in normalization
ratioResult of method getRatio on the complete dataset
result_dataTesting data for vignette
scalingApplies different type of scaling/normalization procedures
scalingFactorSet the endogenous scaling factor associated to an experiment
spikeDatasetspikeDataset constructors function
spikePipeChIP-seq spike-in normalization wrapper function
spikeSummaryOutput dataset summary information
ChIPSeqSpike documentation built on Nov. 8, 2020, 5:29 p.m.