getRatio: Output the percentage of exogenous DNA compared to that of...

In descostesn/ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

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)

descostesn/ChIPSeqSpike documentation built on Aug. 6, 2019, 3:51 p.m.