NAnnotatedDataFrame-class {MSnbase} | R Documentation

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

### Description

An `NAnnotatedDataFrame` is an `"AnnotatedDataFrame"`, as defined in the 'Biobase' package that includes additional labels for multiplexing annotation.

### Objects from the Class

See `"AnnotatedDataFrame"` for object creation with `new`. Multiplexing data is defined by setting the `multiplex` and `multiLables` parameters.

### Slots

`multiplex`:

  Object of class `"numeric"` indicating the number of multiplexed samples described.

`multiLabels`:

  Object of class `"character"` describing the multiplexing.

`varMetadata`:

  Object of class `"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. Inherited from `"AnnotatedDataFrame"`.

`data`:

  Object of class `"data.frame"` containing samples (rows) and measured variables (columns). Inherited from `"AnnotatedDataFrame"`.

`dimLabels`:

  Object of class `"character"` of length 2 that provides labels for the rows and columns in the `show` method. Inherited from `"AnnotatedDataFrame"`.

`.__classVersion__`:

  Object of class `"Versions"` describing the instance version. Intended for developer use. Inherited from `"AnnotatedDataFrame"`.

### Extends

Class `"AnnotatedDataFrame"`, directly. Class `"Versioned"`, by class "AnnotatedDataFrame", distance 2.

### Methods

dim

  `signature(object = "NAnnotatedDataFrame")`: Returns the number of samples, variables and multiplex cardinality in the object.

multiplex

  `signature(object = "NAnnotatedDataFrame")`: Returns the number of multipexed samples described by the object.

multiLabels

  `signature(object = "NAnnotatedDataFrame")`: Returns the multiplex labels.

show

  `signature(object = "NAnnotatedDataFrame")`: Textual description of the object.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### See Also

`"AnnotatedDataFrame"`.

### Examples

    df <- data.frame(x=1:3,
                     y=LETTERS[1:3],
                     row.names=paste("Sample",1:3,sep=""))
    metaData <-
      data.frame(labelDescription=c(
                   "Numbers",
                   "Factor levels"))
    mplx <- c("M1","M2")
    new("NAnnotatedDataFrame",
        data=df,
        varMetadata=metaData,
        multiplex=length(mplx),
        multiLabels=mplx)

[Package MSnbase version 2.4.2 Index]