compileFeatures {netDx} | R Documentation |
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 |
simMetric |
(char) similarity measure to use in converting profiles to interaction networks. |
netSfx |
(char) pattern for finding network files in |
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 |
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()) 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)