Class "moa.sup"

Description

moa.sup class desc.

Objects from the Class

Objects can be created by calls of the form new("moa.sup", ...).

Slots

sup:

Object of class "list", the matrix of supplementary data.

coord.sep:

The projection of geneset infromation on each separate data.

coord.comb:

The projection of geneset infromation on total dataset.

score:

the gene set-sample pathway score

score.data:

the gene set-sample pathway score, data separate

score.pc:

the gene set-sample pathway score, PC separate

score.sep:

the gene set-sample pathway score, separate.

p.val:

the p value matrix have the same dimension with score matrix.

Methods

There is no generic function for objects of "moa.sup", but have specific function, including: - decompose.gs.ind - box.gs.feature - plotGS - decompose.gs.group

Author(s)

Chen Meng

See Also

objects to See Also as decompose.gs.ind, box.gs.feature, plotGS, decompose.gs.group.

Examples

	showClass("moa.sup")
	data(NCI60_4array_supdata)
	data(NCI60_4arrays)

	sapply(NCI60_4array_supdata, dim)
	ana <- moa(NCI60_4arrays, proc.row = "center_ssq1", w.data = "inertia", statis = TRUE)
	plot(ana, value="eig")
	smoa <- sup.moa(ana, sup=NCI60_4array_supdata, nf=5)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mogsa)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mogsa/moa.sup-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: moa.sup-class
> ### Title: Class '"moa.sup"'
> ### Aliases: moa.sup-class
> ### Keywords: classes
> 
> ### ** Examples
> 
> 	showClass("moa.sup")
Class "moa.sup" [package "mogsa"]

Slots:
                                                                        
Name:         sup  coord.sep coord.comb      score score.data   score.pc
Class:        ANY        ANY        ANY        ANY        ANY        ANY
                            
Name:   score.sep      p.val
Class:        ANY        ANY
> 	data(NCI60_4array_supdata)
> 	data(NCI60_4arrays)
> 
> 	sapply(NCI60_4array_supdata, dim)
     agilent hgu133 hgu133p2 hgu95
[1,]     300    298      268   288
[2,]     150    150      150   150
> 	ana <- moa(NCI60_4arrays, proc.row = "center_ssq1", w.data = "inertia", statis = TRUE)
> 	plot(ana, value="eig")
> 	smoa <- sup.moa(ana, sup=NCI60_4array_supdata, nf=5)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>