scalingFactor {ChIPSeqSpike} | R Documentation

## Set the endogenous scaling factor associated to an experiment

### Description

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

### Usage

    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

### Arguments

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

### Details

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.

### Value

The modified object is returned

### Author(s)

Nicolas Descostes

### See Also

`exogenousScalingFactor` `estimateScalingFactors`

### Examples

    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)
    }

[Package ChIPSeqSpike version 1.10.0 Index]