isDataFrame {made4} | R Documentation

## Converts microarray input data into a data frame suitable for analysis in ADE4.

### Description

Converts input data into a data.frame suitable for analysis in ADE4. This function is called by `bga` and other made4 function

### Usage

    isDataFrame(dataset, pos = FALSE, trans = FALSE)

### Arguments

`dataset` | A `matrix`, `data.frame`, `ExpressionSet` or `marrayRaw-class`. If the input is gene expression data in a `matrix` or `data.frame`. The rows and columns are expected to contain the variables (genes) and cases (array samples) respectively.
`pos` | Logical indicating whether to add an integer to `dataset`, to generate positive `data.frame`. Required for `dudi.coa` or `dudi.nsc`.
`trans` | Logical indicating whether `dataset` should be transposed. Default is `FALSE`.

### Details

`bga` and other functions in made4 call this function and it is generally not necessary to call `isDataFrame` this directly.

isDataFrame calls `asDataFrame`, and will accept a `matrix`, `data.frame`, `ExpressionSet` or `marrayRaw-class or SummarizedExperiment` format. It will also transpose data or add a integer to generate a positive data matrix.

If the input data contains missing values (NA), these must first be removed or imputed (see the R libraries impute() or pamr()).

### Value

Returns a data.frame suitable for analysis by ade4 or made4 functions.

### Author(s)

Aedin Culhane

### See Also

`as` in Bioconductor

### Examples

    data(geneData)
    class(geneData)
    dim(geneData)
    dim(isDataFrame(geneData))
    class(isDataFrame(geneData))

[Package made4 version 1.64.0 Index]