runQuery {netDx}R Documentation

Run a query

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())

[Package netDx version 1.1.4 Index]