RatioSet-class | R Documentation |
This class holds preprocessed data for Illumina methylation microarrays.
## Constructor
RatioSet(Beta = NULL, M = NULL, CN = NULL,
annotation = "", preprocessMethod = "", ...)
## Data extraction / Accessors
## S4 method for signature 'RatioSet'
getBeta(object)
## S4 method for signature 'RatioSet'
getM(object)
## S4 method for signature 'RatioSet'
getCN(object)
## S4 method for signature 'RatioSet'
preprocessMethod(object)
## S4 method for signature 'RatioSet'
annotation(object)
## S4 method for signature 'RatioSet'
pData(object)
## S4 method for signature 'RatioSet'
sampleNames(object)
## S4 method for signature 'RatioSet'
featureNames(object)
object |
A |
Beta |
A matrix of beta values (between zero and one) with each row being a methylation loci and each column a sample. |
M |
A matrix of log-ratios (between minus infinity and infinity) with each row being a methylation loci and each column a sample. |
CN |
An optional matrix of copy number estimates with each row being a methylation loci and each column a sample. |
annotation |
An annotation string, optional. |
preprocessMethod |
A |
... |
For the constructor, additional arguments to be passed to
|
This class inherits from eSet
. Essentially the class
is a representation of a Beta
matrix and/or a M
matrix
and optionally a CN
(copy number) matrix linked to a
pData
data frame.
In addition, an annotation and a preprocessMethod slot is present. The annotation slot describes the type of array and also which annotation package to use. The preprocessMethod slot describes the kind of preprocessing that resulted in this dataset.
For a RatioSet
, M-values are defined as logit2
of the
Beta-values if the M-values are not present in the object. Similarly,
if only M-values are present in the object, Beta-values are
ilogit2
of the M-values.
An object of class RatioSet
for the constructor.
Instances are constructed using the RatioSet
function with the
arguments outlined above.
In the following code, object
is a RatioSet
.
getBeta(object)
, getM(object)
, CN(object)
Get the Beta, M or CN matrix.
getManifest(object)
get the manifest associated with the object.
preprocessMethod(object)
Get the preprocess method character
.
In the following code, object
is a RatioSet
.
combine
:Combines two different RatioSet
,
eventually using the combine
method for eSet
.
Kasper Daniel Hansen khansen@jhsph.edu
eSet
for the basic class structure.
Objects of this class are typically created from an
MethylSet
using ratioConvert
.
showClass("RatioSet")
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