ChIPSeqSpikeCore-class {ChIPSeqSpike} | R Documentation

## ChIPSeqSpikeCore Reference Class

### Description

Main class containing input DNA file paths, scores and binding values. The classes ChIPSeqSpikeDataset and ChIPSeqSpikeDatasetBoost inherit from this class. This class is not used directly in the package but is part of ChIPSeqSpikeDataset and ChIPSeqSpikeDatasetBoost. The constructor should not be used directly.

### Fields

inputBam: File path to the input control BAM file

inputBigWig: File path to the input control BigWig file

inputScalingFactor: Input control scaling factor

inputCount: Input control reads count

plotSetArrayList: List of average binding values

matBindingValList: List of binding values matrices

### Constructor

ChIPSeqSpikeCore(inputBamFile, inputBigWigFile, inputSF = 0, inputNb = 0, SetArrayList = list(), matBindingList = list())

### Arguments

inputBamFile

  String representing the file path to the input control BAM file.

inputBigWigFile

  String representing the file path to the input control bigWig file. (see details)

inputSF

  Numeric scaling factor. Default is 0. (see details)

inputNb

  Numeric read counts. Default is 0. (see details)

SetArrayList

  List of PlotSetArray objects. Default is an empty list. (see details)

matBindingList

  List of binding value matrices. Default is an empty list. (see details)

### Getters

`getBam`

  Returns the input BAM path

`getBigWigFile`

  Returns the input bigWig path

`getScalingFactor`

  Returns the input scaling factor

`getCount`

  Returns the number of reads contained in the input BAM file

`getAverageBindingValues`

  Returns a list of PlotSetArray objects. (see details)

`getMatBindingValues`

  Returns a list of matrices containing binding values. (see details)

### Setters

`scalingFactor`

  Modifies the input scaling factor value

`count`

  Modifies the input count value

`bigWigFile`

  Modifies the input bigWig file path

`averageBindingValues`

  Modifies the PlotSetArray list. (see details)

`matBindingValues`

  Modifies the list of binding value matrices. (see details)

### Details

'inputSF' is the scaling factor that will be applied to the input bigWigFile before input subtraction of the different experiments. 'inputNb' which holds the number of aligned reads is used to calculate the aforementioned factor. Only the endogenous count and factor are needed for the input conversely to the experiments for which both the endogenous/exogenous scaling factors and counts are needed to perform spike-in normalization.

'SetArrayList' contains PlotSetArray objects. The PlotSetArray class is defined in the Bioconductor package 'seqplots' and holds the values that are necessary to plot profiles and heatmaps. These values can be retrieved with the 'getAverageBindingValues' function.

'matBindingList' contains matrices of binding values for each experiment. These values are used to generate boxplots and correlations plots. They are retrieved by calling the function 'BWGFile_summary' of the bioconductor package 'rtracklayer'.

### Author(s)

Nicolas Descostes

### See Also

`Experiment-class` `ExperimentLoaded-class` `ChIPSeqSpikeDatasetBoost-class` `ChIPSeqSpikeDataset-class` `spikeDataset` `PlotSetArray-class`

[Package ChIPSeqSpike version 1.0.0 Index]