bigWigFile {ChIPSeqSpike} | R Documentation

## Set the path to the bigwig file

### Description

Set the path to the input or experiment bigwig file.

### Usage

    bigWigFile(theObject) <- value

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

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

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

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

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

### Arguments

`theObject` | A `ChIPSeqSpikeCore`, `ChIPSeqSpikeDataset`, `ChIPSeqSpikeDatasetBoost`, `Experiment` or `ExperimentLoaded` object
`value` | A string representing a path to a bigwig file

### Details

If the object is ChIPSeqSpikeCore, ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost, bigWigFile will set the path to the input DNA experiment bigwig file corresponding to all experiments defined by the object.

If the object is Experiment or ExperimentLoaded, bigWigFile will set the path to the experiment bigwig file.

### Value

The modified object is returned

### Author(s)

Nicolas Descostes

### 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")

    ## Copying example files
    dir.create("./test_chipseqspike")
    result <- file.copy(bigwig_files, "test_chipseqspike")

    if(.Platform$OS.type != 'windows') {
        csds <- spikePipe(info_file_csv, bam_path, bigwig_path, gff_vec,
                          genome_name, verbose = TRUE,
                          outputFolder = output_folder)
        write("toto", file="./test_chipseqspike/toto.bw")
        getBigWigFile(csds[[1]][[1]])
        bigWigFile(csds[[1]][[1]]) <- "test_chipseqspike/toto.bw"
        getBigWigFile(csds[[1]][[1]])
    }

    unlink("test_chipseqspike/", recursive = TRUE)

[Package ChIPSeqSpike version 1.4.0 Index]