convertArray: A method for converting a type of methylation arrays into a...

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

A method for converting a type of methylation arrays into a virtual array of another type.

Description

A method for converting a type of methylation array into a array of another type. The three generations of Illumina methylation arrays are supported: the 27k, the 450k and the EPIC arrays. Specifically, the 450k array and the EPIC array share many probes in common. For RGChannelSet, this function will convert an EPIC array into a 450k array (or vice-versa) by dropping probes that differ between the two arrays. Because most of the probes on the 27k array have a different chemistry than the 450k and EPIC probes, converting an 27k RGChannelSet into another array is not supported. Each array can be converted into another array at the CpG site level, that is any MethylSet and RatioSet (or GenomicMethylSet and GenomicRatioSet) can be converted to a 27k, 450k or EPIC array. The output array is specified by the outType argument.

Usage

## S4 method for signature 'RGChannelSet'
convertArray(object,
                  outType = c("IlluminaHumanMethylation450k",
                              "IlluminaHumanMethylationEPIC"),
                  verbose = TRUE)
## S4 method for signature 'MethylSet'
convertArray(object,
                  outType = c("IlluminaHumanMethylation450k",
                              "IlluminaHumanMethylationEPIC",
                              "IlluminaHumanMethylation27k"),
                  verbose = TRUE)
## S4 method for signature 'RatioSet'
convertArray(object,
                  outType = c("IlluminaHumanMethylation450k",
                              "IlluminaHumanMethylationEPIC",
                              "IlluminaHumanMethylation27k"),
                  verbose = TRUE)
## S4 method for signature 'GenomicMethylSet'
convertArray(object,
                  outType = c("IlluminaHumanMethylation450k",
                              "IlluminaHumanMethylationEPIC",
                              "IlluminaHumanMethylation27k"),
                  verbose = TRUE)
## S4 method for signature 'GenomicRatioSet'
convertArray(object,
                  outType = c("IlluminaHumanMethylation450k",
                              "IlluminaHumanMethylationEPIC",
                              "IlluminaHumanMethylation27k"),
                  verbose = TRUE)

Arguments

object	The input object.
outType	The array type of the output.
verbose	Should the function be verbose?

Details

FIXME: describe the RGChannelSet conversion.

Value

The output object has the same class as the input object, that is either an RGChannelSet, a MethylSet, a RatioSet, a GemomicMethylSet or a GenomicRatioSet, with the type of the array given by the outType argument.

Author(s)

Jean-Philippe Fortin and Kasper D. Hansen.

Examples

if(require(minfiData)) {
  data(RGsetEx.sub)
  rgSet <- convertArray(RGsetEx.sub, outType = "IlluminaHumanMethylationEPIC")
  rgSet
}

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