scalingFactor: Set the endogenous scaling factor associated to an experiment

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

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)
}

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