AnnotatedDataFrame {Biobase} | R Documentation |
AnnotatedDataFrame
s consist 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
phenoData
and varMetadata
.
None
new("AnnotatedDataFrame")
new("AnnotatedDataFrame", data=data.frame(), varMetadata=data.frame())
AnnotatedDataFrame
instances are created using new
. The
initialize method takes two arguments, data
and
varMetadata
. 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.
Class-specific slots:
data
:data.frame
containing samples (rows)
and measured variables (columns).varMetadata
:data.frame
with number of rows
equal number of columns in data
, and at least one column,
named labelDescription
, containing a textual description
of each variable.Class-specific methods.
combine(<AnnotatedDataFrame>,
<AnnotatedDataFrame>
:AnnotatedDataFrame
to a second
AnnotatedDataFrame
, returning the result as an
AnnotatedDataFrame
. Row (sample) names in each argument
must be unique. Variable names present in both arguments occupy a
single column in the resulting AnnotatedDataFrame
. Variable
names unique to either argument create columns with values
assigned for those samples where the variable is
present. varMetadata
in the returned
AnnotatedDataFrame
is updated to reflect the combination.pData(<AnnotatedDataFrame>)
,
pData(<AnnotatedDataFrame>)<-<data.frame>
:AnnotatedDataFrame
varMetadata(<AnnotatedDataFrame>)
,
varMetadata(<AnnotatedDataFrame>)<-<data.frame>
:AnnotatedDataFrame
sampleNames(<AnnotatedDataFrame>)
,
sampleNames(<AnnotatedDataFrame>)<-<data.frame>
:AnnotatedDataFrame
varLabels(<AnnotatedDataFrame>)
,
varLabels(<AnnotatedDataFrame>)<-<data.frame>
:AnnotatedDataFrame
Standard generic methods:
initialize(<AnnotatedDataFrame>)
:new
; not to be called directly by the user.coerce(<phenoData>,<AnnotatedDataFrame>)
:phenoData-class
objects to
AnnotatedDataFrame
, issuing warnings as appropriate.validObject(<AnnotatedDataFrame>)
:data
and
varMetadata
elementsshow(<AnnotatedDataFrame>)
[<sample>,<variable>
:AnnotatedDataFrame
, i.e., including relevant metadata.[[<sample>
, $<-<sample>
:[[<-<new_sample>
:$<sample>
:dim(<AnnotatedDataFrame>)
,
ncol(<AnnotatedDataFrame>)
:dim
) and variables (ncol
) in the
argument.V.J. Carey, after initial design by R. Gentleman