combineArrays | R Documentation |
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.
## 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)
object1 |
The first object. |
object2 |
The second object. |
outType |
The array type of the output. |
verbose |
Should the function be verbose? |
FIXME: describe the RCChannelSet combination.
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.
Jean-Philippe Fortin and Kasper D. Hansen.
if(require(minfiData) && require(minfiDataEPIC)) {
data(RGsetEx.sub)
data(RGsetEPIC)
rgSet <- combineArrays(RGsetEPIC, RGsetEx.sub)
rgSet
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.