Description Objects from the Class Slots Extends Methods Author(s) See Also Examples
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 of‘features’. 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 [<features>,
<samples>]
). Selection and subsetting occur so that relevant
phenotypic data is maintained by the selection or subset.
Objects can be created by calls of the form NChannelSet(
assayData, phenoData, ...)
. See the examples below.
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
.
The data
component of the AnnotatedDataFrame
is
data.frame
with number of rows equal to the number of
samples. Columns of the data
component correspond to measured
covariates.
The varMetadata
component consists of mandatory columns
labelDescription
(providing a textual description of each column
label in the data
component) and channel
. The channel
of varMetadata
is a factor
, with levels equal to the names
of the assayData
channels, plus the special symbol
_ALL_
. The channel
column is used to indicate which
channel(s) the corresponding column in the data
component
of AnnotatedDataFrame
correspond; the _ALL_
symbol
indicates that the data
column is applicable to all
channels. varMetadata
may contain additional columns with
arbitrary information.
Once created, NChannelSet
coordinates selection and subsetting
of channels in phenoData
.
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 the annotation
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 the annotation
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. See
classVersion
and updateObject
for
examples of use.
Class "eSet"
, directly.
Class "VersionedBiobase"
, by class "eSet", distance 2.
Class "Versioned"
, by class "eSet", distance 3.
Methods with class-specific functionality:
channel(object, name, ...)
signature(object="NChannelSet", name="character")
.
Return an ExperessionSet
created from the channel and
corresponding phenotype of argument name
. name
must
have length 1. Arguments ...
are rarely used, but are
passed to the ExpressionSet
constructor, for instance
to influence storage.mode
.
channelNames(object)
, channelNames(object) <- value
signature(object = "NChannelSet")
.
Obtain, reorder, or rename channels contained in
object
. See channelNames
.
selectChannels(object, names, ...
signature(object = "NChannelSet", names = "character")
.
Create a new NChannelSet
from object
, containing
only channels in names
. The ...
is not used by this
method.
object[features, samples]
signature(object = "NChannelSet",
features = "ANY", samples = "ANY")
.
Create a new NChannelSet
from object
, containing
only elements matching features
and samples
; either
index may be missing, or a character, numeric, or logical vector.
sampleNames(object) <- value
signature(object = "NChannelSet", value = "list")
assign
each (named) element of value
to the sampleNames
of
the correspondingly named elements of assayData
in
object
.
Methods with functionality derived from 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)
Martin Morgan <mtmorgan@fhcrc.org>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ## 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")]
|
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