ChIPSeqSpikeCore: ChIPSeqSpikeCore Reference Class

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

View source: R/constructors.R

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


ChIPSeqSpike documentation built on Nov. 8, 2020, 5:29 p.m.