bet.coinertia {made4} | R Documentation

## Between class coinertia analysis

### Description

Between class coinertia analysis. `cia` of 2 datasets where covariance between groups or classes of cases, rather than individual cases are maximised.

### Usage

    bet.coinertia(df1, df2, fac1, fac2, cia.nf = 2, type = "nsc", ...)

### Arguments

`df1` | First 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.
`df2` | Second 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.
`fac1` | A `factor` or `vector` which describes the classes in df1.
`fac2` | A `factor` or `vector` which describes the classes in df2.
`cia.nf` | Integer indicating the number of coinertia analysis axes to be saved. Default value is 2.
`type` | A character string, accepted options are type="nsc" or type="pca".
`...` | further arguments passed to or from other methods.

### Value

A list of class `bet.cia` of length 5

`coin` | An object of class 'coinertia', sub-class `dudi`. See `coinertia`
`coa1, pca1` | An object of class 'nsc' or 'pca', with sub-class 'dudi'. See `dudi`, `dudi.pca` or `dudi.nsc`
`coa2, pca2` | An object of class 'nsc' or 'pca', with sub-class 'dudi'. See `dudi`, `dudi.pca` or `dudi.nsc`
`bet1` | An object of class 'bga', with sub-class 'dudi'. See `dudi`, `bga` or `bca`
`bet2` | An object of class 'bga', with sub-class 'dudi'. See `dudi`, `bga` or `bca`.

### Note

This is very computational intensive. The authors of ade4 are currently re-writing the code for coinertia analysis, so that it should substantially improve the computational requirements (May 2004).

### Author(s)

Aedin Culhane

### References

Culhane AC, et al., 2003 Cross platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics. 4:59

### See Also

See Also as `coinertia`, `cia`.

### Examples

    ### NEED TO DO
    if (require(ade4, quiet = TRUE)) {}

[Package made4 version 1.68.0 Index]