exportBigWigs {ChIPSeqSpike} | R Documentation

## Export bigwig files from values contained in a boost mode object

### Description

In boost mode, binding values of experiments are stored in the form of GRanges tables in the object. exportBigWigs output these values giving a proper bigwig file name corresponding to the transformations already performed.

### Usage

    exportBigWigs(theObject, verbose = TRUE)

    ## S4 method for signature 'ChIPSeqSpikeDatasetBoost'
    exportBigWigs(theObject, verbose = TRUE)

    ## S4 method for signature 'ChIPSeqSpikeDatasetListBoost'
    exportBigWigs(theObject,
    verbose = TRUE)

### Arguments

`theObject` | `ChIPSeqSpike` dataset in boost mode (see ?spikeDataset)
`verbose` | If FALSE, do not output processing messages. Default is TRUE

### Value

Output bigwig files of binding values.

The suffix of the bigwig file reflects the transformation steps performed on the object. If all steps were performed, the file name will be of the form: 'expName-RPM-BGSub-reverse-spiked.bw'. The suffixes 'RPM', 'BGSub', 'reverse' and 'spiked' stands for RPM scaling, input subtraction, RPM scaling reversal and exogenous scaling respectively.

### Methods (by class)

- `ChIPSeqSpikeDatasetBoost`: Method for signature theObject= 'ChIPSeqSpikeDatasetBoost'

- `ChIPSeqSpikeDatasetListBoost`: Method for signature theObject= 'ChIPSeqSpikeDatasetListBoost'

### Author(s)

Nicolas Descostes

### Examples

    ## Mock example on a restricted number of reads
    info_file_csv <- system.file("extdata/info.csv", package="ChIPSeqSpike")
    bam_path <- system.file(c("extdata/bam_files"), package="ChIPSeqSpike")
    bigwig_path <- system.file(c("extdata/bigwig_files"), package="ChIPSeqSpike")

    if(.Platform$OS.type != 'windows') {
        csds <- spikeDataset(infoFile = info_file_csv, bamPath = bam_path,
                             bigWigPath = bigwig_path, boost = TRUE)

        ## Creating test folder
        dir.create("./test_chipseqspike")

        csds <- estimateScalingFactors(csds)

        ## Apply RPM scaling
        csds <- scaling(csds, outputFolder = "test_chipseqspike")

        ## output RPM scaled files
        exportBigWigs(csds)

        ## Apply input subtraction
        csds <- inputSubtraction(csds)

        ## output input subtracted files
        exportBigWigs(csds)

        ## Delete all files generated in this example
        unlink("test_chipseqspike/", recursive = TRUE)
    }

[Package ChIPSeqSpike version 1.12.0 Index]