ExperimentLoaded-class {ChIPSeqSpike} | R Documentation

## ExperimentLoaded Reference Class

### Description

Class inheriting from Experiment and containing loaded binding values

### Fields

loadedBigWigFile: GRanges object representing binding values

endogenousBam: File path to the experiment BAM file aligned to the reference genome

exogenousBam: File path to the experiment BAM file aligned to the exogenous genome

bigWigFile: File path to the experiment BIGWIG file aligned to the reference genome

expName: Experiment name

endogenousScalingFactor: Experiment scaling factor

exogenousScalingFactor: Scaling factor obtained from exogenous DNA

endoCount: Number of reads contained in the endogenous BAM file

exoCount: Number of reads contained in the exogenous BAM file

### Constructor

ExperimentLoaded(endogenousBamFilePath, exogenousBamFilePath, bigWigFilePath, name, endoScalingFactor = 0, exoScalingFactor = 0, endoNb = 0, exoNb = 0, verbose = TRUE)

### Arguments

endogenousBamFilePath

  Character vector of path to experiment BAM file aligned to the reference genome.

exogenousBamFilePath

  Character vector of path to experiment BAM file aligned to the exogenous genome.

bigWigFilePath

  Character vector of path to experiment bigWig file aligned to the reference genome.

name

  Character vector of the experiment name.

endoScalingFactor

  Numeric scaling factor computed from the number of reads aligned to the reference genome. Default is 0.

exoScalingFactor

  Numeric scaling factor computed from the number of reads aligned to the exogenous genome. Default is 0.

endoNb

  Number of reads aligned to the reference genome. Default is 0.

exoNb

  Number of reads aligned to the exogenous genome. Default is 0.

verbose

  Indicate if processing messages should be output. Default is TRUE.

### Getters

`getBam`

  Returns the endogenous BAM path

`getExogenousBam`

  Returns the exogenous BAM path

`getBigWigFile`

  Returns the endogenous bigWig path

`getExpName`

  Returns a character vector of the experiment name

`getScalingFactor`

  Returns the endogenous scaling factor

`getExogenousScalingFactor`

  Returns the exogenous scaling factor

`getCount`

  Returns the number of reads aligned to the reference genome

`getExoCount`

  Returns the number of reads aligned to the exogenous genome

`getLoadedData`

  Returns the GRanges object of binding values

### Setters

`bigWigFile`

  Modifies the endogenous bigWig file path

`loadedData`

  Modifies the GRanges object of binding values

### Details

On Windows operating system, due to the Bioconductor package rtracklayer >= 1.37.6 not supporting bigWig files, this class is not available.

### Author(s)

Nicolas Descostes

### See Also

`Experiment-class` `ChIPSeqSpikeDatasetBoost-class` `spikeSummary` `getRatio`

### 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"),
                            package="ChIPSeqSpike")

    if(.Platform$OS.type != 'windows') {
        exp <- ExperimentLoaded(endogenousBamFilePath = file_vec[2],
                                exogenousBamFilePath = file_vec[1],
                                bigWigFilePath = file_vec[3],
                                name = "H3K79me2_0")
    }

[Package ChIPSeqSpike version 1.8.0 Index]