spikeSummary: Output dataset summary information

In descostesn/ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

Description

Output a table giving endogenous/exogenous scaling scores and read counts for each experiment contained in a dataset

Usage

    spikeSummary(theObject)

## S4 method for signature 'Experiment'
spikeSummary(theObject)
## S4 method for signature 'ExperimentLoaded'
spikeSummary(theObject)
## S4 method for signature 'ChIPSeqSpikeDataset'
spikeSummary(theObject)
## S4 method for signature 'ChIPSeqSpikeDatasetList'
spikeSummary(theObject)
## S4 method for signature 'ChIPSeqSpikeDatasetBoost'
spikeSummary(theObject)
## S4 method for signature 'ChIPSeqSpikeDatasetListBoost'
spikeSummary(theObject)

Arguments

theObject

ChIPSeqSpike dataset (see ?spikeDataset)

Details

The rows represent an experiment (with corresponding input below) and the columns represent the endogenous scaling factor (endoScalFact), the exogenous scaling factor (exoScalFact), the number of reads aligned to the reference genome (endoCount) and the number of reads aligned to the exogenous genome (exoCount).

Value

a matrix of information about each experiment

Methods (by class)

• Experiment: Method for signature theObject = 'Experiment'

• ExperimentLoaded: Method for signature theObject = 'ExperimentLoaded'

• ChIPSeqSpikeDataset: Method for signature theObject= 'ChIPSeqSpikeDataset'

• ChIPSeqSpikeDatasetBoost: Method for signature theObject= 'ChIPSeqSpikeDatasetBoost'

• ChIPSeqSpikeDatasetList: Method for signature theObject= 'ChIPSeqSpikeDatasetList'

• ChIPSeqSpikeDatasetListBoost: Method for signature theObject= 'ChIPSeqSpikeDatasetListBoost'

Author(s)

Nicolas Descostes

See Also

getRatio

Examples

data("result_estimateScalingFactors")
spikeSummary(csds)

descostesn/ChIPSeqSpike documentation built on Aug. 6, 2019, 3:51 p.m.