ExperimentLoaded-class: ExperimentLoaded Reference Class

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

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")
}

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