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

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

Class inheriting from Experiment and containing loaded binding values

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

ExperimentLoaded(endogenousBamFilePath, exogenousBamFilePath, bigWigFilePath, name, endoScalingFactor = 0, exoScalingFactor = 0, endoNb = 0, exoNb = 0, verbose = TRUE)

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.

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

bigWigFile: Modifies the endogenous bigWig file path
loadedData: Modifies the GRanges object of binding values

On Windows operating system, due to the Bioconductor package rtracklayer >= 1.37.6 not supporting bigWig files, this class is not available.

Nicolas Descostes

Experiment-class ChIPSeqSpikeDatasetBoost-class spikeSummary getRatio

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")
}