runQuery {netDx} | R Documentation |
Run a query
runQuery(dbPath, queryFiles, resDir, verbose = TRUE, JavaMemory = 6L, numCores = 1L, debugMode = FALSE)
dbPath |
(char) path to directory with GeneMANIA generic database |
queryFiles |
(list(char)) paths to query files |
resDir |
(char) path to output directory |
verbose |
(logical) print messages |
JavaMemory |
(integer) Memory for GeneMANIA (in Gb) - a total of numCores*GMmemory will be used and distributed for all GM threads |
numCores |
(integer) number of CPU cores for parallel processing |
debugMode |
(logical) when TRUE runs jobs in serial instead of parallel and prints verbose messages. Also prints system Java calls. |
(char) path to GeneMANIA query result files with patient similarity rankings (*PRANK) and feature weights (*NRANK) of results file
dbPath <- system.file("extdata","dbPath",package="netDx") queryFile <- system.file("extdata","GM_query.txt",package="netDx") runQuery(dbPath, queryFile,tempdir())