convertArray | R Documentation |
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.
## 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)
object |
The input object. |
outType |
The array type of the output. |
verbose |
Should the function be verbose? |
FIXME: describe the RGChannelSet conversion.
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.
Jean-Philippe Fortin and Kasper D. Hansen.
if(require(minfiData)) {
data(RGsetEx.sub)
rgSet <- convertArray(RGsetEx.sub, outType = "IlluminaHumanMethylationEPIC")
rgSet
}
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