phenoData {Biobase} | R Documentation

## Class For Patient or Experiment Level Data

### Description

The class consists of a `data.frame` and some accompanying methods suited to handle patient level data for microarrays.

### Creating Objects

`new('phenoData', pData = [data.frame], varLabels = [list], varMetadata = [data.frame])`

### Slots

`pData`:
  Object of class 'data.frame'. The data.
`varLabels`:
  Object of class 'list'. Obtional long labels for the different variables.
`varMetadata`:
  Object of class 'data.frame'. A data frame with a column named varNames and arbitrarily many additional columns.

### Methods

Class-specific methods:

`addVarMetadataEntry(phenoData, character, character, ANY)`
  Not documented: FIXME: it should be a replace method, otherwise it is not clear how should it work
`combine(phenoData, phenoData)`
  Combines several instances into a single 'phenoData' instance. See `combine`
`convertVarLabels(phenoData)`
  Not documented
`getVarMetadata(phenoData, character, character)` or `getVarMetadata(phenoData, character, missing)`
  Not documented
`getUnits(phenoData, character`
  Not documented
`pData(phenoData), pData(phenoData)<-`
  Get/set methods for slot `pData`
`phenoData(exprSet)<-`
  A replacement method for the `phenoData` slot
`split(phenoData, vector)`
  FIXME: there is no implementation!!! A method to `split` `pData` and return a list of `phenoData` objects. Unlike `split` this function requires the number of rows of `pData` to be a multiple of the length of `vector`
`varLabels(phenoData)`
  A method to display the variable labels.
`varMetadata(phenoData)`
  Not documented

Standard methods defined for 'phenoData':

`$(name), $(name, value)<-`
  An old-style method to get and set. It is `pData(object)[[as.character(val)]]` which does not quite have the right semantics but it is close. This operator extracts the named component of the `pData` slot in `phenoData`.
`[(phenoData)`
  A subset operator
`[[(phenoData), [[(phenoData)<-`
  A get/set subset operator
`show(phenoData)`
  Displays the data in a readable manner

Functions defined in Biobase to operate with 'phenoData' instances include:

`df2pD(x, varLabels, varMetadata)`
  Function to coerce from a `data.frame` to a `phenoData` object. Here `x` is the `data.frame` to be coerced; `varLabels` is a character describing each of the columns in `x` and `varMetadata` is a more extensive descriptions of the variables in `x`, including units of measurement etc
`read.phenoData`
  See help on `read.phenoData`

### See Also

`read.phenoData`, `combine`

### Examples

    data(eset)
    pes <- phenoData(eset)
    pes <- convertVarLabels(pes)
    varMetadata(pes)
    pes <- addVarMetadataEntry(pes, "cov1", "units", "inches")
    getUnits(pes, "cov1")

       # example for 'df2pD'
       data(cars)
       d1 = df2pD(cars)

[Package Biobase version 1.9.2 Index]