# ChIP-Seq data scaling according to spike-in control

## Documentation for package ‘ChIPSeqSpike’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G I M P R S misc

## -- A --

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

## -- B --

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

## -- C --

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

## -- D --

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

## -- E --

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

## -- G --

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

## -- I --

inputSubtraction | Substracts binding scores of input DNA to experiment binding scores
inputSubtraction-method | Substracts binding scores of input DNA to experiment binding scores

## -- M --

matBindingValues | Set the matrices of binding values
matBindingValues<- | Set the matrices of binding values
matBindingValues<--method | Set the matrices of binding values

## -- P --

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

## -- R --

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

## -- S --

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

## -- misc --

[[-method | ChIPSeqSpikeDataset Reference Class
[[-method | ChIPSeqSpikeDatasetList Reference Class
[[-method | ChIPSeqSpikeDatasetListBoost Reference Class
[[<--method | ChIPSeqSpikeDataset Reference Class
[[<--method | ChIPSeqSpikeDatasetList Reference Class
[[<--method | Experiment Reference Class