setupFeatureDB {netDx} | R Documentation

## setup database of features for feature selection

### Description

Creates all the input files for the collection of features used in feature selection.

### Usage

    setupFeatureDB(pheno, prepDir = tempdir())

### Arguments

`pheno` | (data.frame) patient metadata. Must contain ID column
`prepDir` | (char) directory in which to setup database

### Value

(data.frame) internal numerical id for patients (INTERNAL_ID) and user-provided ID (ID)

### Examples

    data(xpr,pheno)
    pathwayList <- list(pathA=rownames(xpr)[1:10],pathB=rownames(xpr)[21:50])

    dataList <- list(rna=xpr)  #only one layer type
    groupList <- list(rna=pathwayList) # group genes by pathways

    makeNets <- function(dataList, groupList, netDir,...) {
        netList <- makePSN_NamedMatrix(dataList[['rna']],
    		rownames(dataList[['rna']]),
         groupList[['rna']],netDir,verbose=FALSE,
    			writeProfiles=TRUE,...)
        unlist(netList)
    }
    tmpDir <- tempdir(); netDir <- paste(tmpDir,"nets",sep=getFileSep())
    dir.create(netDir,recursive=TRUE)

    pheno_id <- setupFeatureDB(pheno,netDir)

[Package netDx version 1.0.3 Index]