R: Class "dimRedData"

dimRedData-class {dimRed} | R Documentation

## Class "dimRedData"

### Description

A class to hold data for dimensionality reduction and methods.

### Usage

    ## S4 method for signature 'dimRedData'
    as.data.frame(x, meta.prefix = "meta.",
      data.prefix = "")

    ## S4 method for signature 'formula'
    as.dimRedData(formula, data)

    ## S4 method for signature 'dimRedData'
    getData(object)

    ## S4 method for signature 'dimRedData'
    getMeta(object)

    ## S4 method for signature 'dimRedData'
    nrow(x)

    ## S4 method for signature 'dimRedData,ANY,ANY,ANY'
    x[i]

    ## S4 method for signature 'dimRedData'
    ndims(object)

### Arguments

`x` | Of class dimRedData
`meta.prefix` | Prefix for the columns of the meta data names.
`data.prefix` | Prefix for the columns of the variable names.
`formula` | The formula, left hand side is assigned to the meta slot right hand side is assigned to the data slot.
`data` | A data frame
`object` | Of class dimRedData.
`i` | a valid index for subsetting rows.

### Details

The class hast two slots, `data` and `meta`. The `data` slot contains a `numeric matrix` with variables in columns and observations in rows. The `meta` slot may contain a `data.frame` with additional information. Both slots need to have the same number of rows or the `meta` slot needs to contain an empty `data.frame`.

See examples for easy conversion from and to `data.frame`.

For plotting functions see `plot.dimRedData`.

### Methods (by generic)

- `as.data.frame`: convert to data.frame

- `as.dimRedData`: Convert a `data.frame` to a dimRedData object using a formula

- `getData`: Get the data slot.

- `getMeta`: Get the meta slot.

- `nrow`: Get the number of observations.

- `[`: Subset rows.

- `ndims`: Extract the number of Variables from the data.

### Slots

`data`

  of class `matrix`, holds the data, observations in rows, variables in columns

`meta`

  of class `data.frame`, holds meta data such as classes, internal manifold coordinates, or simply additional data of the data set. Must have the same number of rows as the `data` slot or be an empty data frame.

### Examples

    ## Load an example data set:
    s3d <- loadDataSet("3D S Curve")

    ## Create using a constructor:

    ### without meta information:
    dimRedData(iris[, 1:4])

    ### with meta information:
    dimRedData(iris[, 1:4], iris[, 5])

    ### using slot names:
    dimRedData(data = iris[, 1:4], meta = iris[, 5])

    ## Convert to a dimRedData objects:
    Iris <- as(iris[, 1:4], "dimRedData")

    ## Convert to data.frame:
    head(as(s3d, "data.frame"))
    head(as.data.frame(s3d))
    head(as.data.frame(as(iris[, 1:4], "dimRedData")))

    ## Extract slots:
    head(getData(s3d))
    head(getMeta(s3d))

    ## Get the number of observations:
    nrow(s3d)

    ## Subset:
    s3d[1:5, ]

    ## create a dimRedData object using a formula
    as.dimRedData(Species ~ Sepal.Length + Sepal.Width + Petal.Length + Petal.Width,
                  iris)[1:5]

    ## Shuffle data:
    s3 <- s3d[nrow(s3d)]

    ## Get the number of variables:
    ndims(s3d)

[Package dimRed version 0.1.0 Index]