AnnotatedDataFrame {Biobase} | R Documentation

## Class Containing Measured Variables and Their Meta-Data Description.

### 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`.

### 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 the `show` method.

`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.

`.__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` to `data.frame`.

`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`

`featureNames(<AnnotatedDataFrame>)`, `featureNames(<AnnotatedDataFrame>)<-<ANY>`:

  Set and retrieve the feature names in `AnnotatedDataFrame`; a synonym for `sampleNames`.

`sampleNames(<AnnotatedDataFrame>)`, `sampleNames(<AnnotatedDataFrame>)<-<ANY>`:

  Set and retrieve the sample names in `AnnotatedDataFrame`

`varLabels(<AnnotatedDataFrame>)`, `varLabels(<AnnotatedDataFrame>)<-<data.frame>`:

  Set and retrieve the variable labels in the `AnnotatedDataFrame`

`dimLabels(<AnnotatedDataFrame>)`, `dimLabels(<AnnotatedDataFrame>) <- <character>`

  Retrieve labels used for display of `AnnotatedDataFrame`, e.g., ‘rowNames’, ‘columnNames’.

Standard generic methods:

`initialize(<AnnotatedDataFrame>)`:

  Object instantiation, used by `new`; not to be called directly by the user.

`as(<data.frame>, "AnnotatedDataFrame")`:

  Convert a `data.frame` to an AnnotatedDataFrame.

`as(<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

`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(<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. Unlike a `data.frame`, setting `drop=TRUE` generates an error.

`[[<variable>`, `$<variable>`:

  Selector returning a variable (column of `pData`).

`[[<variable>, ...]]<-<new_value>`, `$<variable> <- <new_value>`:

  Replace or add a variable to `pData`. ... can include named arguments (especially `labelDescription`) to be added to `varMetadata`.

`head(<AnnotatedDataFrame>, n = 6L, ...)`, `tail(<AnnotatedDataFrame>, n=6L, ...)`

  Select the first (last for tail) `n` rows; negative `n` returns the first (last) `nrow() - n` rows.

`dim(<AnnotatedDataFrame>)`, `ncol(<AnnotatedDataFrame>)`:

  Number of samples and variables (`dim`) and variables (`ncol`) in the argument.

`dimnames(<AnnotatedDataFrame>)`, `rownames(<AnnotatedDataFrame>)`, `colnames(<AnnotatedDataFrame>)`:

  row and column names.

### Author(s)

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

### See Also

`eSet`, `ExpressionSet`, `read.AnnotatedDataFrame`

### 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)

[Package Biobase version 2.40.0 Index]