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.
`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 1.0.3 Index]