getCount: Get the number of reads aligned to the endogenous reference...

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

Description

Access and returns the number of reads of an experiment or input DNA experiment that were aligned to the endogenous reference genome.

Usage

getCount(theObject)
            
            
## S4 method for signature 'ChIPSeqSpikeDataset'
getCount(theObject)

## S4 method for signature 'ChIPSeqSpikeDatasetBoost'
getCount(theObject)

## S4 method for signature 'Experiment'
getCount(theObject)

## S4 method for signature 'ExperimentLoaded'
getCount(theObject)

## S4 method for signature 'ChIPSeqSpikeCore'
getCount(theObject)

Arguments

theObject

A ChIPSeqSpikeCore, ChIPSeqSpikeDataset, ChIPSeqSpikeDatasetBoost, Experiment or ExperimentLoaded object

Details

If the object is ChIPSeqSpikeCore, ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost, getCount returns the number of reads of the input DNA experiment that were aligned to the endogenous reference genome.

If the object is Experiment or ExperimentLoaded, getCount returns the number of reads of the experiment that were aligned to the endogenous reference genome.

Value

A numeric of the number of reads aligned to the endogenous reference genome

Author(s)

Nicolas Descostes

See Also

getExoCount

Examples

data(result_extractBinding)
getCount(csds[[1]])

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