IlluminaMethylationManifest-class | R Documentation |
"IlluminaMethylationManifest"
This is a class for representing an Illumina methylation microarray design, ie. the physical location and the probe sequences. This information should be independent of genome build and annotation.
## Constructor
IlluminaMethylationManifest(TypeI = DataFrame(),
TypeII = DataFrame(),
TypeControl = DataFrame(),
TypeSnpI = DataFrame(),
TypeSnpII = DataFrame(),
annotation = "")
## Data extraction
## S4 method for signature 'IlluminaMethylationManifest'
getManifest(object)
## S4 method for signature 'character'
getManifest(object)
getProbeInfo(object, type = c("I", "II", "Control",
"I-Green", "I-Red", "SnpI", "SnpII"))
getManifestInfo(object, type = c("nLoci", "locusNames"))
getControlAddress(object, controlType = c("NORM_A", "NORM_C",
"NORM_G", "NORM_T"),
asList = FALSE)
object |
Either an object of class
|
TypeI |
A |
TypeII |
A |
TypeControl |
A |
TypeSnpI |
A |
TypeSnpII |
A |
annotation |
An annotation |
type |
A single character describing what kind of information
should be returned. For |
controlType |
A character vector of control types. |
asList |
If |
An object of class IlluminaMethylationManifest
for the constructor.
The data
slot contains the following objects: TypeI
,
TypeII
and TypeControl
which are all of class
data.frame
, describing the array design.
Methylation loci of type I are measured using two different probes, in
either the red or the green channel. The columns AddressA
,
AddresB
describes the physical location of the two probes on
the array (with ProbeSeqA
, ProbeSeqB
giving the probe
sequences), and the column Color
describes which color channel
is used.
Methylation loci of type II are measured using a single probe, but with two different color channels. The methylation signal is always measured in the green channel.
In the following code, object
is a IlluminaMethylationManifest
.
getManifest(object)
Get the manifest object.
getProbeInfo(object)
Returns a DataFrame
giving the type I, type II or control probes. It is also possible
to get the type I probes measured in the Green or Red channel. This
function ensures that the return object only contains probes which
are part of the input object. In case of a RGChannelSet
and
type I probes, both addresses needs to be in the object.
getManifestInfo(object)
Get some information about the manifest object (the chip design).
getControlAddress(object)
Get the control addresses for control probes of a certain type.
getControlTypes(object)
Returns the types and the numbers of control probes of each type.
Kasper Daniel Hansen khansen@jhsph.edu.
IlluminaMethylationAnnotation
for annotation
information for the array (information depending on a specific genome
build).
if(require(IlluminaHumanMethylation450kmanifest)) {
show(IlluminaHumanMethylation450kmanifest)
head(getProbeInfo(IlluminaHumanMethylation450kmanifest, type = "I"))
head(IlluminaHumanMethylation450kmanifest@data$TypeI)
head(IlluminaHumanMethylation450kmanifest@data$TypeII)
head(IlluminaHumanMethylation450kmanifest@data$TypeControl)
}
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