runQuery: Run a query

In BaderLab/netDx: Network-based patient classifier

Description

Run a query

Usage

runQuery(
  dbPath,
  queryFiles,
  resDir,
  verbose = TRUE,
  JavaMemory = 6L,
  numCores = 1L,
  debugMode = FALSE
)

Arguments

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.

Value

(char) path to GeneMANIA query result files with patient similarity rankings (*PRANK) and feature weights (*NRANK) of results file

Examples

dbPath <- system.file("extdata","dbPath",package="netDx")
queryFile <- system.file("extdata","GM_query.txt",package="netDx")
runQuery(dbPath, queryFile,tempdir())

BaderLab/netDx documentation built on Sept. 26, 2021, 9:13 a.m.