Get the endogenous reference genome binding scores of an experiment

Description

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

Usage

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

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

Arguments

Details

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.

Value

A GRanges object of binding scores

Author(s)

Nicolas Descostes

Examples

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)
}