getBam: Get the path to an endogenous experiment bam file

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

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]])

ChIPSeqSpike documentation built on Nov. 8, 2020, 5:29 p.m.