AnnotatedDataFrame {Biobase}R Documentation

Class to Contain Measured Variables and Their Meta-Data Description.

Description

AnnotatedDataFrames 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.

Extends

None

Creating Objects

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.

Slots

Class-specific slots:

data:
A data.frame containing samples (rows) and measured variables (columns).
varMetadata:
A 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.

Methods

Class-specific methods.

combine(<AnnotatedDataFrame>, <AnnotatedDataFrame>:
Bind data from one 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>:
Set and retrieve the data (samples and variables) in the AnnotatedDataFrame
varMetadata(<AnnotatedDataFrame>), varMetadata(<AnnotatedDataFrame>)<-<data.frame>:
Set and retrieve the meta-data (variables and their descriptions) in the AnnotatedDataFrame
sampleNames(<AnnotatedDataFrame>), sampleNames(<AnnotatedDataFrame>)<-<data.frame>:
Set and retrieve the sample names in the AnnotatedDataFrame
varLabels(<AnnotatedDataFrame>), varLabels(<AnnotatedDataFrame>)<-<data.frame>:
Set and retrieve the variable labels in the AnnotatedDataFrame

Standard generic methods:

initialize(<AnnotatedDataFrame>):
Object instantiation, used by new; not to be called directly by the user.
coerce(<phenoData>,<AnnotatedDataFrame>):
Convert old-style phenoData-class objects to AnnotatedDataFrame, issuing warnings as appropriate.
validObject(<AnnotatedDataFrame>):
Validity-checking method, ensuring coordination between data and varMetadata elements
show(<AnnotatedDataFrame>)
Abbreviated display of object
[<sample>,<variable>:
Subset operation, taking two arguments and indexing the sample and variable. Returns an AnnotatedDataFrame, i.e., including relevant metadata.
[[<sample>, $<-<sample>:
Selector returning a sample and measured variables.
[[<-<new_sample>:
Replace a sample row of data.
$<sample>:
Selector returning a sample and measured variables.
dim(<AnnotatedDataFrame>), ncol(<AnnotatedDataFrame>):
Number of samples and variables (dim) and variables (ncol) in the argument.

Author(s)

V.J. Carey, after initial design by R. Gentleman

See Also

eSet, ExpressionSet


[Package Biobase version 1.10.1 Index]