getBam {ChIPSeqSpike} | R Documentation

## Get the path to an endogenous experiment bam file

### Description

Access and returns the path to the bam file containing the reads of an experiment aligned to the endogenous reference genome.

### Usage

    getBam(theObject)

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

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

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

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

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

### Arguments

`theObject` | A `ChIPSeqSpikeCore`, `ChIPSeqSpikeDataset`, `ChIPSeqSpikeDatasetBoost`, `Experiment` or `ExperimentLoaded` object

### Details

If the object is ChIPSeqSpikeCore, ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost, getBam returns the path to the input DNA experiment bam file containing reads aligned to the endogenous reference genome.

If the object is Experiment or ExperimentLoaded, getBam returns the path to the experiment bam file containing reads aligned to the endogenous reference genome.

### Value

A string of the path to the endogenous bam file

### Author(s)

Nicolas Descostes

### See Also

`getExogenousBam`

### Examples

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

[Package ChIPSeqSpike version 1.10.0 Index]