combineArrays: A method for combining different types of methylation arrays...

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

A method for combining different types of methylation arrays into a virtual array.

Description

A method for combining different types of methylation arrays into a virtual array. 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. This function combines data from the two different array types and outputs a data object of the user-specified type. Essentially, this new object will be like (for example) an EPIC array with many probes missing.

Usage

## S4 method for signature 'RGChannelSet,RGChannelSet'
combineArrays(object1, object2,
                  outType = c("IlluminaHumanMethylation450k",
                              "IlluminaHumanMethylationEPIC"),
                  verbose = TRUE)
## S4 method for signature 'MethylSet,MethylSet'
combineArrays(object1, object2,
                  outType = c("IlluminaHumanMethylation450k",
                              "IlluminaHumanMethylationEPIC",
                              "IlluminaHumanMethylation27k"),
                  verbose = TRUE)
## S4 method for signature 'RatioSet,RatioSet'
combineArrays(object1, object2,
                  outType = c("IlluminaHumanMethylation450k",
                              "IlluminaHumanMethylationEPIC",
                              "IlluminaHumanMethylation27k"),
                  verbose = TRUE)
## S4 method for signature 'GenomicMethylSet,GenomicMethylSet'
combineArrays(object1, object2,
                  outType = c("IlluminaHumanMethylation450k",
                              "IlluminaHumanMethylationEPIC",
                              "IlluminaHumanMethylation27k"),
                  verbose = TRUE)
## S4 method for signature 'GenomicRatioSet,GenomicRatioSet'
combineArrays(object1, object2,
                  outType = c("IlluminaHumanMethylation450k",
                              "IlluminaHumanMethylationEPIC",
                              "IlluminaHumanMethylation27k"),
                  verbose = TRUE)

Arguments

object1	The first object.
object2	The second object.
outType	The array type of the output.
verbose	Should the function be verbose?

Details

FIXME: describe the RCChannelSet combination.

Value

The output object has the same class as the two input objects, 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) && require(minfiDataEPIC)) {
  data(RGsetEx.sub)
  data(RGsetEPIC)
  rgSet <- combineArrays(RGsetEPIC, RGsetEx.sub)
  rgSet
}

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