ChIPSeqSpikeDataset-class: ChIPSeqSpikeDataset Reference Class

In descostesn/ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

Description

Main class containing file paths, scores and values for spike normalization. It inherits from ChIPSeqSpikeCore.

Fields

experimentList: A list of Experiment objects

Constructor

ChIPSeqSpikeDataset(endogenousBam_vec, exogenousBam_vec, bigWigFile_endogenous_vec, inputBigWigFile, inputBamFile, expnames, inputSF = 0, inputNb = 0, SetArrayList = list(), matBindingList = list())

Arguments

endogenousBam_vec

Character vector of file paths to the BAM files aligned to the reference genome.

exogenousBam_vec

Character vector of file paths to the BAM files aligned to the exogenous genome.

bigWigFile_endogenous_vec

Character vector of file paths to the bigWig files aligned to the reference genome.

inputBigWigFile

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

inputBamFile

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

expnames

Character vector of experiment names. (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

getExperimentListBigWigs

Returns a character vector of paths to the experiment bigWig files

getExpName

Returns a character vector of experiment names

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)

x[[i]]

Get the Experiment object at index i

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)

x[[i]] <- value

Set value to ChIPSeqSpikeDataset i

Details

'expnames' character vector is used to define the names of the experiment list and are used as labels in plotting, summary and getRatio functions.

'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'.

If the dataset contains more than one input, one would want to use the ChIPSeqSpikeDatasetList class. Boost mode classes (ChIPSeqSpikeDatasetBoost and ChIPSeqSpikeDatasetListBoost) can also be considered to speed up the analysis.

Author(s)

Nicolas Descostes

See Also

Experiment-class ChIPSeqSpikeCore-class ChIPSeqSpikeDatasetBoost-class ChIPSeqSpikeDatasetList-class spikeDataset PlotSetArray-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", 
                        "bigwig_files/input_0-filtered.bw", 
                        "bam_files/input_0_hg19-filtered.bam"),
                        package="ChIPSeqSpike")

csds <- ChIPSeqSpikeDataset(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")
csds

descostesn/ChIPSeqSpike documentation built on Aug. 6, 2019, 3:51 p.m.