GenomicMethylSet-class | R Documentation |
This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location.
## Constructor
GenomicMethylSet(gr = GRanges(), Meth = new("matrix"),
Unmeth = new("matrix"), annotation = "",
preprocessMethod = "", ...)
## Data extraction / Accessors
## S4 method for signature 'GenomicMethylSet'
getMeth(object)
## S4 method for signature 'GenomicMethylSet'
getUnmeth(object)
## S4 method for signature 'GenomicMethylSet'
getBeta(object, type = "", offset = 0, betaThreshold = 0)
## S4 method for signature 'GenomicMethylSet'
getM(object, type = "", ...)
## S4 method for signature 'GenomicMethylSet'
getCN(object, ...)
## S4 method for signature 'GenomicMethylSet'
pData(object)
## S4 method for signature 'GenomicMethylSet'
sampleNames(object)
## S4 method for signature 'GenomicMethylSet'
featureNames(object)
## S4 method for signature 'GenomicMethylSet'
annotation(object)
## S4 method for signature 'GenomicMethylSet'
preprocessMethod(object)
## S4 method for signature 'GenomicMethylSet'
mapToGenome(object, ...)
object |
A |
gr |
A |
Meth |
A matrix of methylation values (between zero and infinity) with each row being a methylation loci and each column a sample. |
Unmeth |
See the |
annotation |
An annotation character string. |
preprocessMethod |
A preprocess method character string. |
type |
How are the values calculated? For |
offset |
Offset in the beta ratio, see detail. |
betaThreshold |
Constrains the beta values to be in the inverval
betwen |
... |
For the constructor, additional arguments to be passed to
|
For a detailed discussion of getBeta
and getM
see the
deatils section of MethylSet
.
An object of class GenomicMethylSet
for the constructor.
Instances are constructed using the GenomicMethylSet
function with the
arguments outlined above.
A number of useful accessors are inherited from
RangedSummarizedExperiment
.
In the following code, object
is a GenomicMethylSet
.
getMeth(object)
, getUnmeth(object)
Get the Meth or Unmeth matrix.
getBeta(object)
Get Beta, see details.
getM(object)
get M-values, see details.
getCN(object)
get copy number values which are defined as the sum of the methylation and unmethylation channel.
getManifest(object)
get the manifest associated with the object.
sampleNames(object)
, featureNames(object)
Get the sampleNames (colnames) or the featureNames (rownames).
preprocessMethod(object)
,
annotation(object)
Get the preprocess method or annotation
character
.
mapToGenome(object)
Since object
is already
mapped to the genome, this method simply returns object
unchanged.
combine
:Combines two different GenomicMethylSet
,
eventually using the cbind
method for SummarizedExperiment
.
Kasper Daniel Hansen khansen@jhsph.edu
RangedSummarizedExperiment
in the
SummarizedExperiment package for the basic class structure.
Objects of this class are typically created by using the function
mapToGenome
on a MethylSet
.
showClass("GenomicMethylSet")
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