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Last data update: 2014.03.03

R: Projection of supplementary data onto axes from a between...

suppl

R Documentation

Projection of supplementary data onto axes from a between group analysis

Description

Projection and class prediction of supplementary points onto axes from a between group analysis, bga.

Usage

suppl(dudi.bga, supdata, supvec = NULL, assign=TRUE, ...)
## S3 method for class 'suppl'
plot(x, dudi.bga, axis1=1, axis2=2, supvec=sup$true.class, supvec.pred= sup$predicted, ...)

Arguments

`dudi.bga`	An object returned by `bga`.
`supdata`	Test or blind dataset. Accepted formats are a `matrix`, `data.frame`, `ExpressionSet` or `marrayRaw-class`.
`supvec`	A factor or vector which describes the classes in the training dataset.
`supvec.pred`	A factor or vector which describes the classes which were predicted by `suppl`.
`assign`	A logical indicating whether class assignment should be calculated using the method described by Culhane et al., 2002. The default value is `TRUE`.
`x`	An object returned by `suppl`.
`axis1`	Integer, the column number for the x-axis. The default is 1.
`axis2`	Integer, the column number for the y-axis. The default is 2.
`...`	further arguments passed to or from other methods.

Details

After performing a between group analysis on a training dataset using bga, a test dataset can be then projected onto bga axes using suppl.

suppl returns the projected coordinates and assignment of each test case (array).

The test dataset must contain the same number of variables (genes) as the training dataset. The input format of both the training dataset and test dataset are verified using array2ade4. Use plot.bga to plot results from bga.

Value

A list containing:

suppl

An object returned by suppl

Author(s)

Aedin Culhane

References

Culhane AC, et al., 2002 Between-group analysis of microarray data. Bioinformatics. 18(12):1600-8.

Examples

data(khan)
#khan.bga<-bga(khan$train, khan$train.classes)
if (require(ade4, quiet = TRUE)) {
khan.bga<-bga.suppl(khan$train, supdata=khan$test, classvec=khan$train.classes, 
          supvec=khan$test.classes)

khan.bga
plot.bga(khan.bga, genelabels=khan$annotation$Symbol)
khan.bga$suppl

plot.suppl(khan.bga$suppl, khan.bga) 
plot.suppl(khan.bga$suppl, khan.bga, supvec=NULL, supvec.pred=NULL)
plot.suppl(khan.bga$suppl, khan.bga, axis1=2, axis2=3,supvec=NULL, supvec.pred=NULL)
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(made4)
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/made4/suppl.Rd_%03d_medium.png", width=480, height=480)
> ### Name: suppl
> ### Title: Projection of supplementary data onto axes from a between group
> ###   analysis
> ### Aliases: suppl plot.suppl
> ### Keywords: manip multivariate
> 
> ### ** Examples
> 
> data(khan)
> #khan.bga<-bga(khan$train, khan$train.classes)
> if (require(ade4, quiet = TRUE)) {
+ khan.bga<-bga.suppl(khan$train, supdata=khan$test, classvec=khan$train.classes, 
+           supvec=khan$test.classes)
+ 
+ khan.bga
+ plot.bga(khan.bga, genelabels=khan$annotation$Symbol)
+ khan.bga$suppl
+ 
+ plot.suppl(khan.bga$suppl, khan.bga) 
+ plot.suppl(khan.bga$suppl, khan.bga, supvec=NULL, supvec.pred=NULL)
+ plot.suppl(khan.bga$suppl, khan.bga, axis1=2, axis2=3,supvec=NULL, supvec.pred=NULL)
+ }
[1] "Need to specify groups"
[1] "Need to specify groups"
[1] "Need to specify groups"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>