buildMACAT: Create MACAT list from objects in workspace

Description

This is a wrapper around the preprocessedLoader function. Use it, when you want to build a MACAT-list structure from objects already in your workspace.

Usage

buildMACAT(matrix, chip, labels = NULL, chromLocObj = NULL)

Arguments

matrix

expression matrix with rows=genes and columns=samples; Rownames have to match chip; Columnnames are not mandatory.

chip

Identifier for used microarray

labels

Classlabels for samples, has to have length=number of columns in matrix

chromLocObj

Object of class chromLocation specifying the genomic position, each probe on the array is mapped to. If not provided, it is build in the function using annotate's function buildChromLocation.

Value

A MACAT-list structure. For an example and a description of the format see data stjude in package 'stjudem'.

Details

This is only a convenience wrapper around the function preprocessedLoader for the case, that you want to build a MACAT-list from objects in your workspace.

Examples

Run this code

 X <- matrix(rnorm(200),nrow=20,ncol=10)
 rownames(X) <- c('34916_s_at','34917_at','34462_at','163_at','35219_at',
	'31641_s_at','33300_at','33301_g_at','38950_r_at','41249_at',
	'294_s_at','32004_s_at','33299_at','41243_at','33341_at','362_at',
	'1918_at','41499_at','41500_at','41282_s_at')
 colnames(X) <- paste("Sample",1:10,sep="")
 y <- rep(c("A","B"),c(5,5))
 toy <- buildMACAT(X,"hgu95av2.db",y)
 summary(toy)