experimentList: Set the list of Experiment and ExperimentLoaded objects
In ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

Description Usage Arguments Value Author(s) See Also Examples

Set the list of Experiment and ExperimentLoaded objects to the ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost object

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

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

`theObject`	A ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost object
`value`	A list of Experiment and ExperimentLoaded objects

The modified object is returned

Nicolas Descostes

getExperimentList

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)

    experimentList(csds[[1]]) <- getExperimentList(csds[[1]])

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