bet.coinertia: Between class coinertia analysis

Description Usage Arguments Value Note Author(s) References See Also Examples

Description

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

Usage

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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

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2
### NEED TO DO 
if (require(ade4, quiet = TRUE)) {}

Example output

Loading required package: ade4
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: scatterplot3d
NULL

made4 documentation built on Nov. 1, 2018, 3:44 a.m.