getLoadedData: Get the endogenous reference genome binding scores of an...
In ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

Description Usage Arguments Details Value Author(s) Examples

Accesses and returns the binding scores of an experiment or input DNA experiment on the endogenous reference genome. (only available in boost mode).

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

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

theObject

A ChIPSeqSpikeDatasetBoost or ExperimentLoaded object

If the object is ChIPSeqSpikeDatasetBoost, getLoadedData returns a GRanges object of binding scores of the input DNA experiment.

If the object is ExperimentLoaded, getLoadedData returns a GRanges object of binding scores of the experiment.

A GRanges object of binding scores

Nicolas Descostes

file_vec <- system.file("extdata", 
                        c("bam_files/H3K79me2_0_dm3-filtered.bam", 
                        "bam_files/H3K79me2_0_hg19-filtered.bam", 
                        "bigwig_files/H3K79me2_0-filtered.bw", 
                        "bigwig_files/input_0-filtered.bw", 
                        "bam_files/input_0_hg19-filtered.bam"),
                        package="ChIPSeqSpike")

if(.Platform$OS.type != 'windows') {
    csds <- ChIPSeqSpikeDatasetBoost(endogenousBam_vec = file_vec[2],
                             exogenousBam_vec = file_vec[1],
                             bigWigFile_endogenous_vec = file_vec[3], 
                             inputBigWigFile = file_vec[4], 
                             inputBamFile = file_vec[5], 
                             expnames = "H3K79me2_0")
    getLoadedData(csds)
}