ratioConvert-methods: Converting methylation signals to ratios (Beta or M-values)

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

Converting methylation signals to ratios (Beta or M-values)

Description

Converting methylation data from methylation and unmethylation channels, to ratios (Beta and M-values).

Usage

## S4 method for signature 'MethylSet'
ratioConvert(object, what = c("beta", "M", "both"), keepCN = TRUE, ...)
## S4 method for signature 'GenomicMethylSet'
ratioConvert(object, what = c("beta", "M", "both"), keepCN = TRUE, ...)

Arguments

object	Either a MethylSet, or a GenomicRatioSet.
what	Which ratios should be computed and stored?
keepCN	A logical, should copy number values be computed and stored in the object?
...	Passed to getBeta, getM methods.

Value

An object of class RatioSet or GenomicRatioSet.

Author(s)

Kasper Daniel Hansen [e-mail]

See Also

RatioSet or codeGenomicRatioSet for the output object and MethylSet or codeGenomicMethylSet for the input object.

Examples

if (require(minfiData)) {
  ## MsetEx.sub is a small subset of MsetEx;
  ## only used for computational speed.
  RsetEx.sub <- ratioConvert(MsetEx.sub, keepCN = TRUE)
  }

hansenlab/minfi documentation built on May 3, 2024, 3:49 p.m.