permGPU (version 0.14.9)

makeExprSet: Create an expressionSet object for use with permGPU

Description

The permGPU function expects that the phenotypic and molecular (expression) data are provided as an ExpressionSet. This is a simple utility function that creates this object so that permGPU can be used along with data objects created for use with certain Bioconductor packages.

Usage

makeExprSet(exprdat, phenodat, anno = "custom")

Arguments

exprdat

This should be an $K\times n$, where $K$ denotes the number of markers/features and $n$ denotes the number of patients, expression matrix. It is expected that the $K$ marker names are assigned as row names of this matrix (i.e., could be extracted as rownames(exprdat).

phenodat

This is an $n\times p$ data.frame, $n$ denotes the number of patients and $p$ denotes the number of clinical co-variables. It is assumed that the rows of this data.frame are matched up with the columns of exprdat

anno

This slot can be used to assign a label to the data set.

Value

An object of class ExpressionSet.

See Also

ExpressionSet

Examples

# NOT RUN {
library(Biobase)
set.seed(123)

## Generate toy phenotype and expression data sets
## This example consists of 4 markers and ten patients
n<-10
K<-4
pdat=data.frame(grp=rep(1:0,each=n/2),bp=rnorm(n),ostime=rexp(n),event=rbinom(n,1,0.8))
expdat=matrix(rnorm(K*n),K,n)

## Assign marker names g1,...,gK to the expression data set
## (as row names) and patient ids id1,...,idn to the expression 
## data set (as column names) and phenotype data (as row names)
rownames(expdat)=paste("g",1:K,sep="")
patid=paste("id",1:n,sep="")
rownames(pdat)=patid
colnames(expdat)=patid

## Create the ExprSet object
testdat=makeExprSet(expdat,pdat)
class(testdat)


## Check the dimensions of the expression and phenotype data sets
dim(exprs(testdat))
dim(pData(testdat))

## Get sample and marker ids
sampleNames(testdat)
featureNames(testdat)

# }