AnnotatedDataFrame {Biobase} | R Documentation

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

### Description

`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`.

### 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]