getRatio {ChIPSeqSpike} | R Documentation

## Output the percentage of exogenous DNA compared to that of endogenous DNA

### Description

Output the percentage of exogenous DNA compared to that of endogenous DNA

### Usage

        getRatio(theObject)

    ## S4 method for signature 'Experiment'
    getRatio(theObject)
    ## S4 method for signature 'ExperimentLoaded'
    getRatio(theObject)
    ## S4 method for signature 'ChIPSeqSpikeDataset'
    getRatio(theObject)
    ## S4 method for signature 'ChIPSeqSpikeDatasetList'
    getRatio(theObject)
    ## S4 method for signature 'ChIPSeqSpikeDatasetBoost'
    getRatio(theObject)
    ## S4 method for signature 'ChIPSeqSpikeDatasetListBoost'
    getRatio(theObject)

### Arguments

`theObject` | ChIPSeqSpike dataset (see ?spikeDataset)

### Details

The rows represent, for each experiment of the dataset, the percentage of exogenous DNA defined as the number of aligned exogenous reads compared to the total number of reads.

The method 'getRatio' will throw a warning if the percentage of exogenous DNA represents less than 2 percent or more than 25 percent of the endogenous DNA. Less than 2 percent of exogenous DNA does not guarantee a proper scaling. Large amount of exogenous DNA should not impact the scaling procedure but is worth notifying to the user[1].

### Value

A numeric matrix

### Methods (by class)

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

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

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

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

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

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

### Author(s)

Nicolas Descostes

### References

[1] Orlando et al, "Quantitative ChIP-Seq normalization reveals global modulation of the epigenome", Cell Rep, 2014.

### See Also

`spikeSummary`

### Examples

    ## Mock example on files samples
    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")
    gff_vec <- system.file("extdata/test_coord.gff", package="ChIPSeqSpike")
    genome_name <- "hg19"

    csds <- spikeDataset(infoFile = info_file_csv, bamPath = bam_path,
                         bigWigPath = bigwig_path)
    csds <- estimateScalingFactors(csds)
    getRatio(csds)

    ## Results on the complete files
    data("ratio")
    print(ratio)

[Package ChIPSeqSpike version 1.2.1 Index]