convertArray {minfi} | R Documentation

## 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
    }

[Package minfi version 1.40.0 Index]