NChannelSet-class
Class to contain data from multiple channel array technologies
Container for high-throughput assays and experimental meta-data. Data are from experiments where a single chip contains several (more than 1) different channels. All channels on a chip have the same set offeatures. An experiment consists of a collection of several N-channel chips; each chip is a sample.
An NChannelSet
provides a way to coordinate assay data
(expression values) with phenotype information and references to chip
annotation data; it extends the eSet
class.
An NChannelSet
allows channels to be extracted (using the
channels
method, mentioned below), and subsets of features or
samples to be selected (using [
). Selection and subsetting occur so that relevant
phenotypic data is maintained by the selection or subset.
- Keywords
- classes
Objects from the Class
Objects can be created by calls of the form NChannelSet(
assayData, phenoData, ...)
. See the examples below.
Slots
assayData
:-
Object of class
AssayData
, usually an environment containing matrices of identical size. Each matrix represents a single channel. Columns in each matrix correspond to samples, rows to features. Once created,NChannelSet
manages coordination of samples and channels. phenoData
:-
Object of class
AnnotatedDataFrame
. Thedata
component of theAnnotatedDataFrame
isdata.frame
with number of rows equal to the number of samples. Columns of thedata
component correspond to measured covariates. ThevarMetadata
component consists of mandatory columnslabelDescription
(providing a textual description of each column label in thedata
component) andchannel
. Thechannel
ofvarMetadata
is afactor
, with levels equal to the names of theassayData
channels, plus the special symbol_ALL_
. Thechannel
column is used to indicate which channel(s) the corresponding column in thedata
component ofAnnotatedDataFrame
correspond; the_ALL_
symbol indicates that thedata
column is applicable to all channels.varMetadata
may contain additional columns with arbitrary information. Once created,NChannelSet
coordinates selection and subsetting of channels inphenoData
. featureData
:-
Object of class
AnnotatedDataFrame
, used to contain feature data that is unique to this experiment; feature-level descriptions common to a particular chip are usually referenced through theannotation
slot. experimentData
:-
Object of class
MIAME
containing descriptions of the experiment. annotation
:-
Object of class
"character"
. Usually a length-1 character string identifying the chip technology used during the experiment. The annotation string is used to retrieve information about features, e.g., using theannotation
package. protocolData
:-
Object of class
"character"
. A character vector identifying the dates the samples were scanned during the experiment. .__classVersion__
:-
Object of class
Versions
, containing automatically created information about the class definition Biobase package version, and other information about the user system at the time the instance was created. SeeclassVersion
andupdateObject
for examples of use.
Extends
Class "eSet"
, directly.
Class "VersionedBiobase"
, by class "eSet", distance 2.
Class "Versioned"
, by class "eSet", distance 3.
Methods
Methods with class-specific functionality:
channel(object, name, ...)
-
signature(object="NChannelSet", name="character")
. Return anExperessionSet
created from the channel and corresponding phenotype of argumentname
.name
must have length 1. Arguments...
are rarely used, but are passed to theExpressionSet
constructor, for instance to influencestorage.mode
. channelNames(object)
,channelNames(object) <- value
-
signature(object = "NChannelSet")
. Obtain, reorder, or rename channels contained inobject
. SeechannelNames
. selectChannels(object, names, ...
-
signature(object = "NChannelSet", names = "character")
. Create a newNChannelSet
fromobject
, containing only channels innames
. The...
is not used by this method. object[features, samples]
-
signature(object = "NChannelSet", features = "ANY", samples = "ANY")
. Create a newNChannelSet
fromobject
, containing only elements matchingfeatures
andsamples
; either index may be missing, or a character, numeric, or logical vector. sampleNames(object) <- value
-
signature(object = "NChannelSet", value = "list")
assign each (named) element ofvalue
to thesampleNames
of the correspondingly named elements ofassayData
inobject
.
eSet
:
annotation
, annotation<-
, assayData
,
assayData<-
, classVersion
, classVersion<-
,
dim
, dims
, experimentData
, experimentData<-
,
featureData
, featureData<-
, phenoData
,
phenoData<-
, protocolData
, protocolData<-
,
pubMedIds
, pubMedIds<-
, sampleNames
,
sampleNames<-
, storageMode
, storageMode<-
,
varMetadata
, varMetadata<-
, isCurrent
,
isVersioned
, updateObject
. Additional methods: coerce
(as, to convert between
objects, if possible), initialize
(used internally for
creating objects), show
(invoked automatically when the
object is displayed to the screen)
See Also
eSet
, ExpressionSet
.
Examples
## An empty NChannelSet
obj <- NChannelSet()
## An NChannelSet with two channels (R, G) and no phenotypic data
obj <- NChannelSet(R=matrix(0,10,5), G=matrix(0,10,5))
## An NChannelSet with two channels and channel-specific phenoData
R <- matrix(0, 10, 3, dimnames=list(NULL, LETTERS[1:3]))
G <- matrix(1, 10, 3, dimnames=list(NULL, LETTERS[1:3]))
assayData <- assayDataNew(R=R, G=G)
data <- data.frame(ChannelRData=numeric(ncol(R)),
ChannelGData=numeric(ncol(R)),
ChannelRAndG=numeric(ncol(R)))
varMetadata <- data.frame(labelDescription=c(
"R-specific phenoData",
"G-specific phenoData",
"Both channel phenoData"),
channel=factor(c("R", "G", "_ALL_")))
phenoData <- AnnotatedDataFrame(data=data, varMetadata=varMetadata)
obj <- NChannelSet(assayData=assayData, phenoData=phenoData)
obj
## G channel as NChannelSet
selectChannels(obj, "G")
## G channel as ExpressionSet
channel(obj, "G")
## Samples "A" and "C"
obj[,c("A", "C")]