made4 (version 1.46.0)

bet.coinertia: 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.

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)) {}