RGChannelSet-class | R Documentation |
"RGChannelSet"
These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array.
## Constructors
RGChannelSet(Green = new("matrix"), Red = new("matrix"),
annotation = "", ...)
RGChannelSetExtended(Green = new("matrix"), Red = new("matrix"),
GreenSD = new("matrix"), RedSD = new("matrix"),
NBeads = new("matrix"), annotation = "", ...)
## Accessors
## S4 method for signature 'RGChannelSet'
annotation(object)
## S4 method for signature 'RGChannelSet'
pData(object)
## S4 method for signature 'RGChannelSet'
sampleNames(object)
## S4 method for signature 'RGChannelSet'
featureNames(object)
## S4 method for signature 'RGChannelSet'
getBeta(object, ...)
getGreen(object)
getRed(object)
getNBeads(object)
## S4 method for signature 'RGChannelSet'
getManifest(object)
## Convenience functions
getOOB(object)
getSnpBeta(object)
object |
An |
Green |
A matrix of Green channel values (between zero and infinity) with each row being a methylation loci and each column a sample. |
Red |
See the |
GreenSD |
See the |
RedSD |
See the |
NBeads |
See the |
annotation |
An annotation string, optional. |
... |
For the constructor(s), additional arguments to be passed
to |
An object of class RGChannelSet
or RGChannelSetExtended
for the constructors.
Instances are constructed using the
RGChannelSet
or RGChannelSetExtended
functions with the
arguments outlined above.
as(object, "RGChannelSet")
coerces a
RGChannelSetExtended
object into a RGChannelSet
.
getGreen
:Gets the Green channel as a matrix.
getRed
:Gets the Red channel as a matrix.
getNBeads
:Gets the number of beads as a matrix, this
requires an RGChannelSetExtended
.
getManifest
:Gets the manifest object itself associated with the array type
getOOB
:Retrives the so-called “out-of-band”
(OOB) probes. These are the measurements of Type I probes in the
“wrong” color channel. Return value is a list with two
matrices, named Red
and Grn
.
getSnpBeta
:Retrives the measurements of the 65 SNP probes located on the array. These SNP probes are intended to be used for sample tracking and sample mixups. The return value is a matrix of beta values. Each SNP probe ought to have values clustered around 3 distinct values corresponding to homo-, and hetero-zygotes.
combine
:Combines two different RGChannelSet
,
eventually using the combine
method for eSet
.
The class inherits a number of useful methods from SummarizedExperiment
. In earliers versions of minfi, this class inherited
from eSet
, and we have kept of number of methods related to this, for example pData
.
The best way to access phenotype data and sample names are colData
and colnames
.
Amongst the useful methods are
dim
, nrow
, ncol
The dimension (number of probes by number of samples) of the experiment.
colData
, colnames
, pData
, sampleNames
Phenotype information and sample names.
rownames
, featureNames
This is the addresses (probe identifiers) of the array.
Kasper Daniel Hansen khansen@jhsph.edu
See SummarizedExperiment
for the basic class that is used as a
building block for "RGChannelSet(Extended)"
. See
IlluminaMethylationManifest
for a class representing the
design of the array.
showClass("RGChannelSet")
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