compileFeatures: Create GeneMANIA database
In BaderLab/netDx: Network-based patient classifier

Description Usage Arguments Details Value Examples

Create GeneMANIA database

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

`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()`

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

(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

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())
if (file.exists(netDir)) unlink(netDir,recursive=TRUE)
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)