exoCount {ChIPSeqSpike} | R Documentation

## Set the number of reads associated to an experiment

### Description

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

### Usage

    exoCount(theObject) <- value

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

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

### Arguments

`theObject` | An Experiment or ExperimentLoaded object
`value` | A numeric representing the number of mapped reads to the exogenous reference genome

### Value

The modified object is returned

### Author(s)

Nicolas Descostes

### See Also

`count` `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)
        getExoCount(csds[[1]][[1]])
        exoCount(csds[[1]][[1]]) <- 5
        getExoCount(csds[[1]][[1]])
        unlink("test_chipseqspike/", recursive = TRUE)
    }

[Package ChIPSeqSpike version 1.0.0 Index]