inputSubtraction: Substracts binding scores of input DNA to experiment binding...
In descostesn/ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

Description Usage Arguments Details Value Methods (by class) Author(s) See Also Examples

Substracts binding scores of input DNA to experiment binding scores. This step enables to remove artifactual signal.

inputSubtraction(theObject, verbose = TRUE)
            
            
## S4 method for signature 'ChIPSeqSpikeDataset'
inputSubtraction(theObject, verbose = TRUE)

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

## S4 method for signature 'ChIPSeqSpikeDatasetList'
inputSubtraction(theObject, verbose = TRUE)

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

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

When immunoprecipitating (IP) DNA bound by a given protein, a control is needed to distinguish background noise from true signal. This is typically achieved by performing a mock IP omitting the use of antibody. After sequencing, one can notice peaks of signal above background. These peaks have to be removed from analysis since they represent false positives.

The inputSubtraction function reads bigwig files into GRanges objects that are used to perform the subtraction. In boost mode (ChIPSeqSpikeDatasetBoost and ChIPSeqSpikeDatasetListBoost), The reading/writing steps are omitted.

If not in boost mode, the input DNA subtracted bigwig files are written to the folder containing the currently processed bigwig files. In boost mode, use the method exportBigWigs to output the transformed files.

On Windows operating system, due to the Bioconductor package rtracklayer >= 1.37.6 not supporting bigWig files, this method is not available.

Return an object of the same class of the input object with subtracted experiment scores.

A 'BGSub' suffix is added to the bigwig file name.

ChIPSeqSpikeDataset: Method for signature theObject= 'ChIPSeqSpikeDataset'
ChIPSeqSpikeDatasetBoost: Method for signature theObject= 'ChIPSeqSpikeDatasetBoost'
ChIPSeqSpikeDatasetList: Method for signature theObject= 'ChIPSeqSpikeDatasetList'
ChIPSeqSpikeDatasetListBoost: Method for signature theObject= 'ChIPSeqSpikeDatasetListBoost'

Nicolas Descostes

spikeDataset exportBigWigs spikePipe scaling

## 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)

    ## Copying test files to the current folder
    originalBW_vec <- as.character(getBigWigFile(csds))
    dir.create("./test_chipseqspike")
    result <- file.copy(originalBW_vec, "test_chipseqspike")

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

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

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