scalingFactor: Set the endogenous scaling factor associated to an experiment
In ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

Description Usage Arguments Details Value Author(s) See Also Examples

Set the endogenous scaling factor associated to an experiment or its corresponding input DNA experiment.

scalingFactor(theObject) <- value
            
            
## S4 replacement method for signature 'ChIPSeqSpikeDataset'
scalingFactor(theObject) <- value

## S4 replacement method for signature 'ChIPSeqSpikeDatasetBoost'
scalingFactor(theObject) <- value

## S4 replacement method for signature 'Experiment'
scalingFactor(theObject) <- value

## S4 replacement method for signature 'ExperimentLoaded'
scalingFactor(theObject) <- value

## S4 replacement method for signature 'ChIPSeqSpikeCore'
scalingFactor(theObject) <- value

`theObject`	A `ChIPSeqSpikeCore`, `ChIPSeqSpikeDataset`, `ChIPSeqSpikeDatasetBoost`, `Experiment` or `ExperimentLoaded` object
`value`	A numeric representing the endogenous scaling factor

A scaling factor is defined as:

1/(bam_count/1000000)

If the object is ChIPSeqSpikeCore, ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost, scalingFactor will set the endogenous scaling factor of the input DNA experiment of the dataset.

If the object is Experiment or ExperimentLoaded, scalingFactor will set the endogenous scaling factor of the experiment.

The modified object is returned

Nicolas Descostes

exogenousScalingFactor estimateScalingFactors

info_file_csv <- system.file("extdata/info.csv", package="ChIPSeqSpike")
bam_path <- system.file("extdata/bam_files", package="ChIPSeqSpike")
bigwig_path <- system.file("extdata/bigwig_files", package="ChIPSeqSpike")
gff_vec <- system.file("extdata/test_coord.gff", package="ChIPSeqSpike")
genome_name <- "hg19"
output_folder <- "test_chipseqspike"
bigwig_files <- system.file("extdata/bigwig_files", 
                            c("H3K79me2_0-filtered.bw",
                              "H3K79me2_100-filtered.bw",
                              "H3K79me2_50-filtered.bw",
                              "input_0-filtered.bw",
                              "input_100-filtered.bw",
                              "input_50-filtered.bw"), package="ChIPSeqSpike")

if(.Platform$OS.type != 'windows') {

    ## Copying example files
    dir.create("./test_chipseqspike")
    result <- file.copy(bigwig_files, "test_chipseqspike")

    csds <- spikePipe(info_file_csv, bam_path, bigwig_path, gff_vec, genome_name, 
                      verbose = TRUE, outputFolder = output_folder)

    getScalingFactor(csds[[1]][[1]])
    scalingFactor(csds[[1]][[1]]) <- 15
    getScalingFactor(csds[[1]][[1]])

    unlink("test_chipseqspike/", recursive = TRUE)
}