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

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

Object containing information about experiment. It constitutes an element of a list held by ChIPSeqSpikeDataset class objects

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

Experiment(endogenousBamFilePath, exogenousBamFilePath, bigWigFilePath, name, endoScalingFactor = 0, exoScalingFactor = 0, endoNb = 0, exoNb = 0)

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.
endoNb: Number of reads aligned to the exogenous genome. Default is 0.

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

scalingFactor: Modifies the endogenous scaling factor value
exogenousScalingFactor: Modifies the exogenous scaling factor value
count: Modifies the endogenous count value
exoCount: Modifies the exogenous count value
bigWigFile: Modifies the endogenous bigWig file path
x[[i]] <- value: Set value to experiment i

Nicolas Descostes

ExperimentLoaded-class ChIPSeqSpikeDataset-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")

exp <- Experiment(endogenousBamFilePath = file_vec[2], 
                  exogenousBamFilePath = file_vec[1], 
                  bigWigFilePath = file_vec[3], 
                  name = "H3K79me2_0")