compileFeatures {netDx} | R Documentation

## Create GeneMANIA database

### Description

Create GeneMANIA database

### Usage

    compileFeatures(netDir, outDir = tempdir(), simMetric = "pearson",
      netSfx = "txt$", verbose = TRUE, numCores = 1L,
      P2N_threshType = "off", P2N_maxMissing = 100, JavaMemory = 4L,
      altBaseDir = NULL, debugMode = FALSE, ...)

### Arguments

`netDir` | (char) path to dir with input networks/profiles. All networks in this directory will be added to the GM database. Note: This needs to be an absolute path, not relative.
`outDir` | (char) path to dir in which GeneMANIA database is created. The database will be under `outDir/dataset`.
`simMetric` | (char) similarity measure to use in converting profiles to interaction networks.
`netSfx` | (char) pattern for finding network files in `netDir`.
`verbose` | (logical) print messages
`numCores` | (integer) num cores for parallel processing
`P2N_threshType` | (char) Most users shouldn't have to change this. ProfileToNetworkDriver's threshold option. One of 'off|auto'. unit testing
`P2N_maxMissing` | (integer 5-100)
`JavaMemory` | (integer) Memory for GeneMANIA (in Gb)
`altBaseDir` | (char) Only use this if you're developing netDx. Used in unit tests
`debugMode` | (logical) when TRUE runs jobs in serial instead of parallel and prints verbose messages. Also prints system Java calls and prints all standard out and error output associated with these calls.
`...` | params for `writeQueryBatchFile()`

### Details

Creates a generic_db for use with GeneMania QueryRunner. The database is in tab-delimited format, and indexes are built using Apache lucene. NOTE: This pipeline expects input in the form of interaction networks and not profiles. Profile tables have patient-by-datapoint format (e.g. patient-by-genotype) Interaction networks have pairwise similarity measures: <PatientA> <PatientB><similarity> Documentation: https://github.com/GeneMANIA/pipeline/wiki/GenericDb

### Value

(list). 'dbDir': path to GeneMANIA database 'netDir': path to directory with interaction networks. If profiles are provided, this points to the INTERACTIONS/ subdirectory within the text-based GeneMANIA generic database If the DB creation process results in an erorr, these values return NA

### 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)
    netList <- createPSN_MultiData(dataList=dataList, groupList=groupList,
        pheno=pheno_id,netDir=netDir,customFunc=makeNets,verbose=TRUE)

    outDir <- paste(tmpDir,'dbdir',sep=getFileSep());
    dir.create(outDir)
    dbDir <- compileFeatures(netDir,outDir)

[Package netDx version 1.0.3 Index]