count: Set the number of reads 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 number of endogenous reads associated to an experiment. This is used to compute scaling factors.

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

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

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

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

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

`theObject`	A `ChIPSeqSpikeDataset`, `ChIPSeqSpikeDatasetBoost`, `Experiment`, `ExperimentLoaded` or `ChIPSeqSpikeCore` object
`value`	A numeric representing the number of mapped reads

If the object is ChIPSeqSpikeCore, ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost, count will set the number of input DNA mapped reads to the endogenous reference genome.

If the object is Experiment or ExperimentLoaded, count will set the number of experiment mapped reads to the endogenous reference genome.

The modified object is returned

Nicolas Descostes

exoCount 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)
    getCount(csds[[1]][[1]])
    count(csds[[1]][[1]]) <- 10
    getCount(csds[[1]][[1]])
    unlink("test_chipseqspike/", recursive = TRUE)
}