getCount {ChIPSeqSpike} | R Documentation

## Get the number of reads aligned to the endogenous reference genome

### 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]])

[Package ChIPSeqSpike version 1.12.0 Index]