ChIPSeqSpikeCore: ChIPSeqSpikeCore Reference Class
In ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

Description Fields Constructor Arguments Getters Setters Details Author(s) See Also

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.

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

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

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)

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)

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)

'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'.

Nicolas Descostes

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