getLoadedData {ChIPSeqSpike} | R Documentation

## 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

`theObject` | A `ChIPSeqSpikeDatasetBoost` or `ExperimentLoaded` object

### 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)
    }

[Package ChIPSeqSpike version 1.12.0 Index]