API for descostesn/ChIPSeqSpike
ChIP-Seq data scaling according to spike-in control

Global functions
ChIPSeqSpikeCore Man page Source code
ChIPSeqSpikeCore-class Man page
ChIPSeqSpikeDataset Man page Source code
ChIPSeqSpikeDataset-class Man page
ChIPSeqSpikeDatasetBoost Man page Source code
ChIPSeqSpikeDatasetBoost-class Man page
ChIPSeqSpikeDatasetList Man page Source code
ChIPSeqSpikeDatasetList-class Man page
ChIPSeqSpikeDatasetListBoost Man page Source code
ChIPSeqSpikeDatasetListBoost-class Man page
Experiment Man page Source code
Experiment-class Man page
ExperimentLoaded Man page Source code
ExperimentLoaded-class Man page
[[,ChIPSeqSpikeDataset,ANY,ANY-method Man page
[[,ChIPSeqSpikeDatasetList,ANY,ANY-method Man page
[[,ChIPSeqSpikeDatasetListBoost,ANY,ANY-method Man page
[[<-,ChIPSeqSpikeDataset,ANY,ANY-method Man page
[[<-,ChIPSeqSpikeDatasetList,ANY,ANY-method Man page
[[<-,Experiment,ANY,ANY-method Man page
averageBindingValues Man page
averageBindingValues<- Man page
averageBindingValues<-,ChIPSeqSpikeCore-method Man page
averageBindingValues<-,ChIPSeqSpikeDataset-method Man page
averageBindingValues<-,ChIPSeqSpikeDatasetBoost-method Man page
bigWigFile Man page
bigWigFile<- Man page
bigWigFile<-,ChIPSeqSpikeCore-method Man page
bigWigFile<-,ChIPSeqSpikeDataset-method Man page
bigWigFile<-,ChIPSeqSpikeDatasetBoost-method Man page
bigWigFile<-,Experiment-method Man page
bigWigFile<-,ExperimentLoaded-method Man page
boxplotSpike Man page
boxplotSpike,ChIPSeqSpikeDataset-method Man page
boxplotSpike,ChIPSeqSpikeDatasetBoost-method Man page
boxplotSpike,ChIPSeqSpikeDatasetList-method Man page
boxplotSpike,ChIPSeqSpikeDatasetListBoost-method Man page
callPlot Source code
callRatio Source code
checkPercentages Source code
checkPlotHeatmapsParam Source code
computeBamCount Source code
computeScaling Source code
computeScalingBoost Source code
computeScalingFactor Source code
convertTypes Source code
count Man page
count<- Man page
count<-,ChIPSeqSpikeCore-method Man page
count<-,ChIPSeqSpikeDataset-method Man page
count<-,ChIPSeqSpikeDatasetBoost-method Man page
count<-,Experiment-method Man page
count<-,ExperimentLoaded-method Man page
csds Man page
datasetList Man page
datasetList<- Man page
datasetList<-,ChIPSeqSpikeDatasetList-method Man page
datasetList<-,ChIPSeqSpikeDatasetListBoost-method Man page
estimateScalingFactors Man page
estimateScalingFactors,ChIPSeqSpikeDataset-method Man page
estimateScalingFactors,ChIPSeqSpikeDatasetBoost-method Man page
estimateScalingFactors,ChIPSeqSpikeDatasetList-method Man page
estimateScalingFactors,ChIPSeqSpikeDatasetListBoost-method Man page
estimateScalingFactors,Experiment-method Man page
estimateScalingFactors,ExperimentLoaded-method Man page
exoCount Man page
exoCount<- Man page
exoCount<-,Experiment-method Man page
exoCount<-,ExperimentLoaded-method Man page
exogenousScalingFactor Man page
exogenousScalingFactor<- Man page
exogenousScalingFactor<-,Experiment-method Man page
exogenousScalingFactor<-,ExperimentLoaded-method Man page
experimentList Man page
experimentList<- Man page
experimentList<-,ChIPSeqSpikeDataset-method Man page
experimentList<-,ChIPSeqSpikeDatasetBoost-method Man page
exportBigWigs Man page
exportBigWigs,ChIPSeqSpikeDatasetBoost-method Man page
exportBigWigs,ChIPSeqSpikeDatasetListBoost-method Man page
extractBinding Man page
extractBinding,ChIPSeqSpikeDataset-method Man page
extractBinding,ChIPSeqSpikeDatasetBoost-method Man page
extractBinding,ChIPSeqSpikeDatasetList-method Man page
extractBinding,ChIPSeqSpikeDatasetListBoost-method Man page
getAverageBindingValues Man page
getAverageBindingValues,ChIPSeqSpikeCore-method Man page
getAverageBindingValues,ChIPSeqSpikeDataset-method Man page
getAverageBindingValues,ChIPSeqSpikeDatasetBoost-method Man page
getBam Man page
getBam,ChIPSeqSpikeCore-method Man page
getBam,ChIPSeqSpikeDataset-method Man page
getBam,ChIPSeqSpikeDatasetBoost-method Man page
getBam,Experiment-method Man page
getBam,ExperimentLoaded-method Man page
getBigWigFile Man page
getBigWigFile,ChIPSeqSpikeCore-method Man page
getBigWigFile,ChIPSeqSpikeDataset-method Man page
getBigWigFile,ChIPSeqSpikeDatasetBoost-method Man page
getBigWigFile,ChIPSeqSpikeDatasetList-method Man page
getBigWigFile,Experiment-method Man page
getBigWigFile,ExperimentLoaded-method Man page
getCount Man page
getCount,ChIPSeqSpikeCore-method Man page
getCount,ChIPSeqSpikeDataset-method Man page
getCount,ChIPSeqSpikeDatasetBoost-method Man page
getCount,Experiment-method Man page
getCount,ExperimentLoaded-method Man page
getDatasetList Man page
getDatasetList,ChIPSeqSpikeDatasetList-method Man page
getDatasetList,ChIPSeqSpikeDatasetListBoost-method Man page
getExoCount Man page
getExoCount,Experiment-method Man page
getExoCount,ExperimentLoaded-method Man page
getExogenousBam Man page
getExogenousBam,Experiment-method Man page
getExogenousBam,ExperimentLoaded-method Man page
getExogenousScalingFactor Man page
getExogenousScalingFactor,Experiment-method Man page
getExogenousScalingFactor,ExperimentLoaded-method Man page
getExpName Man page
getExpName,ChIPSeqSpikeDataset-method Man page
getExpName,ChIPSeqSpikeDatasetBoost-method Man page
getExpName,Experiment-method Man page
getExpName,ExperimentLoaded-method Man page
getExperimentList Man page
getExperimentList,ChIPSeqSpikeDataset-method Man page
getExperimentList,ChIPSeqSpikeDatasetBoost-method Man page
getExperimentListBigWigs Man page
getExperimentListBigWigs,ChIPSeqSpikeDataset-method Man page
getExperimentListBigWigs,ChIPSeqSpikeDatasetBoost-method Man page
getLoadedData Man page
getLoadedData,ChIPSeqSpikeDatasetBoost-method Man page
getLoadedData,ExperimentLoaded-method Man page
getMatBindingValues Man page
getMatBindingValues,ChIPSeqSpikeCore-method Man page
getMatBindingValues,ChIPSeqSpikeDataset-method Man page
getMatBindingValues,ChIPSeqSpikeDatasetBoost-method Man page
getRatio Man page
getRatio,ChIPSeqSpikeDataset-method Man page
getRatio,ChIPSeqSpikeDatasetBoost-method Man page
getRatio,ChIPSeqSpikeDatasetList-method Man page
getRatio,ChIPSeqSpikeDatasetListBoost-method Man page
getRatio,Experiment-method Man page
getRatio,ExperimentLoaded-method Man page
getScalingFactor Man page
getScalingFactor,ChIPSeqSpikeCore-method Man page
getScalingFactor,ChIPSeqSpikeDataset-method Man page
getScalingFactor,ChIPSeqSpikeDatasetBoost-method Man page
getScalingFactor,Experiment-method Man page
getScalingFactor,ExperimentLoaded-method Man page
inputSubtraction Man page
inputSubtraction,ChIPSeqSpikeDataset-method Man page
inputSubtraction,ChIPSeqSpikeDatasetBoost-method Man page
inputSubtraction,ChIPSeqSpikeDatasetList-method Man page
inputSubtraction,ChIPSeqSpikeDatasetListBoost-method Man page
loadCorrelationPlot Source code
loadExtractionOnList Source code
loadInputSubtractionList Source code
loadOnList Source code
loadScalingOnList Source code
matBindingValues Man page
matBindingValues<- Man page
matBindingValues<-,ChIPSeqSpikeCore-method Man page
matBindingValues<-,ChIPSeqSpikeDataset-method Man page
matBindingValues<-,ChIPSeqSpikeDatasetBoost-method Man page
modifyBigWigName Source code
notFoundMessage Source code
perform_boxplot_violinplot Source code
perform_heatscatterplot Source code
plotAverageProfiles Source code
plotCor Man page
plotCor,ChIPSeqSpikeDataset-method Man page
plotCor,ChIPSeqSpikeDatasetBoost-method Man page
plotCor,ChIPSeqSpikeDatasetList-method Man page
plotCor,ChIPSeqSpikeDatasetListBoost-method Man page
plotHeatmaps Man page
plotHeatmaps,ChIPSeqSpikeDataset-method Man page
plotHeatmaps,ChIPSeqSpikeDatasetBoost-method Man page
plotHeatmaps,ChIPSeqSpikeDatasetList-method Man page
plotHeatmaps,ChIPSeqSpikeDatasetListBoost-method Man page
plotLegends Source code
plotProfile Man page
plotProfile,ChIPSeqSpikeDataset-method Man page
plotProfile,ChIPSeqSpikeDatasetBoost-method Man page
plotProfile,ChIPSeqSpikeDatasetList-method Man page
plotProfile,ChIPSeqSpikeDatasetListBoost-method Man page
plotSpiked Source code
plotTransform Man page
plotTransform,ChIPSeqSpikeDataset-method Man page
plotTransform,ChIPSeqSpikeDatasetList-method Man page
ratio Man page
removingNABigWig Source code
result_data Man page
result_estimateScalingFactors Man page
result_extractBinding Man page
retrieveAllFiles Source code
retrieveAverageValuesList Source code
retrieveIndexes Source code
retrieveIndexesFromAllTypes Source code
retrieveMatBindingList Source code
retrieveMeanBindingValues Source code
retrieveSF Source code
scaling Man page
scaling,ChIPSeqSpikeDataset-method Man page
scaling,ChIPSeqSpikeDatasetBoost-method Man page
scaling,ChIPSeqSpikeDatasetList-method Man page
scaling,ChIPSeqSpikeDatasetListBoost-method Man page
scalingFactor Man page
scalingFactor<- Man page
scalingFactor<-,ChIPSeqSpikeCore-method Man page
scalingFactor<-,ChIPSeqSpikeDataset-method Man page
scalingFactor<-,ChIPSeqSpikeDatasetBoost-method Man page
scalingFactor<-,Experiment-method Man page
scalingFactor<-,ExperimentLoaded-method Man page
spikeDataset Man page Source code
spikePipe Man page Source code
spikeSummary Man page
spikeSummary,ChIPSeqSpikeDataset-method Man page
spikeSummary,ChIPSeqSpikeDatasetBoost-method Man page
spikeSummary,ChIPSeqSpikeDatasetList-method Man page
spikeSummary,ChIPSeqSpikeDatasetListBoost-method Man page
spikeSummary,Experiment-method Man page
spikeSummary,ExperimentLoaded-method Man page
subtractScores Source code
summaryDatasetList Source code
validateBigWig Source code
validateMatBindingValList Source code
validateParameters Source code
validatePath Source code
validatePlotSetArrayList Source code
validateSFAndCount Source code
verifyDataset Source code
descostesn/ChIPSeqSpike documentation built on Jan. 29, 2018, 3 p.m.