AnnotatedDataFrame
Class Containing Measured Variables and Their Meta-Data Description.
An AnnotatedDataFrame
consists of two parts. There is a collection
of samples and the values of variables measured on those
samples. There is also a description of each variable measured. The
components of an AnnotatedDataFrame
can be accessed with
pData
and varMetadata
.
- Keywords
- classes
Extends
Versioned
Creating Objects
AnnotatedDataFrame(data, varMetadata, dimLabels=c("rowNames", "columnNames"), ...)
AnnotatedDataFrame
instances are created using
AnnotatedDataFrame
. The function can take three arguments, data
is a
data.frame
of the samples (rows) and measured variables
(columns). varMetadata
is a data.frame
with the number
of rows equal to the number of columns of the data
argument.
varMetadata
describes aspects of each measured
variable. dimLabels
provides aesthetic control for labeling rows
and columns in the show
method. varMetadata
and
dimLabels
can be missing. as(data.frame, "AnnotatedDataFrame")
coerces a data.frame
to an
AnnotatedDataFrame
. annotatedDataFrameFrom
may be a convenient way to create
an AnnotatedDataFrame
from AssayData-class
.
Slots
Class-specific slots:
data
:- A
data.frame
containing samples (rows) and measured variables (columns). dimLabels
:- A
character
vector of length 2 that provides labels for the rows and columns in theshow
method. varMetadata
:- A
data.frame
with number of rows equal number of columns indata
, and at least one column, namedlabelDescription
, containing a textual description of each variable. .__classVersion__
:- A
Versions
object describing the R and Biobase version numbers used to created the instance. Intended for developer use.
Methods
Class-specific methods.
as(annotatedDataFrame, "data.frame")
- Coerce objects of
AnnotatedDataFrame
todata.frame
. combine(
:, - Bind data from one
AnnotatedDataFrame
to a secondAnnotatedDataFrame
, returning the result as anAnnotatedDataFrame
. Row (sample) names in each argument must be unique. Variable names present in both arguments occupy a single column in the resultingAnnotatedDataFrame
. Variable names unique to either argument create columns with values assigned for those samples where the variable is present.varMetadata
in the returnedAnnotatedDataFrame
is updated to reflect the combination. pData(
,) pData(
:)<- - Set and
retrieve the data (samples and variables) in the
AnnotatedDataFrame
varMetadata(
,) varMetadata(
:)<- - Set and
retrieve the meta-data (variables and their descriptions) in the
AnnotatedDataFrame
featureNames(
,) featureNames(
:)<- - Set and
retrieve the feature names in
AnnotatedDataFrame
; a synonym forsampleNames
. sampleNames(
,) sampleNames(
:)<- - Set and
retrieve the sample names in
AnnotatedDataFrame
varLabels(
,) varLabels(
:)<- - Set and
retrieve the variable labels in the
AnnotatedDataFrame
-
dimLabels(
,) dimLabels(
) <- - Retrieve
labels used for display of
AnnotatedDataFrame
, e.g., rowNames, columnNames.
initialize(
:) - Object instantiation, used
by
new
; not to be called directly by the user. as(
:, "AnnotatedDataFrame") - Convert a
data.frame
to an AnnotatedDataFrame. as(
:, ) - Convert
old-style
phenoData-class
objects toAnnotatedDataFrame
, issuing warnings as appropriate. validObject(
:) - Validity-checking
method, ensuring coordination between
data
andvarMetadata
elements updateObject(object, ..., verbose=FALSE)
- Update instance to current version, if necessary. See
updateObject
isCurrent(object)
- Determine whether version of object is current. See
isCurrent
isVersioned(object)
- Determine whether object contains a 'version' string describing its structure . See
isVersioned
show(
) - Abbreviated display of object
[
:, - Subset operation, taking two arguments and
indexing the sample and variable. Returns an
AnnotatedDataFrame
, i.e., including relevant metadata. Unlike adata.frame
, settingdrop=TRUE
generates an error. [[
,$
:- Selector returning a
variable (column of
pData
). [[
,, ...]]<- $
:<- - Replace or add a variable to
pData
. ... can include named arguments (especiallylabelDescription
) to be added tovarMetadata
. dim(
,) ncol(
:) - Number of samples and
variables (
dim
) and variables (ncol
) in the argument. dimnames(
,) rownames(
,) colnames(
:) - row and column names.
See Also
Examples
df <- data.frame(x=1:6,
y=rep(c("Low", "High"),3),
z=I(LETTERS[1:6]),
row.names=paste("Sample", 1:6, sep="_"))
metaData <-
data.frame(labelDescription=c(
"Numbers",
"Factor levels",
"Characters"))
AnnotatedDataFrame()
AnnotatedDataFrame(data=df)
AnnotatedDataFrame(data=df, varMetadata=metaData)
as(df, "AnnotatedDataFrame")
obj <- AnnotatedDataFrame()
pData(obj) <- df
varMetadata(obj) <- metaData
validObject(obj)