exogenousScalingFactor: Set the exogenous scaling factor associated to an experiment

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

Description

Set the exogenous scaling factor associated to an experiment

Usage

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

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

Arguments

theObject	An Experiment or ExperimentLoaded object
value	A numeric representing the exogenous scaling factor

Details

A scaling factor is defined as:

• 1/(bam_count/1000000)

Value

The modified object is returned

Author(s)

Nicolas Descostes

See Also

scalingFactor 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)
    getExogenousScalingFactor(csds[[1]][[1]])
    exogenousScalingFactor(csds[[1]][[1]]) <- 5
    getExogenousScalingFactor(csds[[1]][[1]])
    unlink("test_chipseqspike/", recursive = TRUE)
}

ChIPSeqSpike documentation built on Nov. 8, 2020, 5:29 p.m.