convertProfileToNetworks {netDx} | R Documentation

## Convert profiles to interaction networks before integration

### Description

Convert profiles to interaction networks before integration

### Usage

    convertProfileToNetworks(netDir, outDir = tempdir(),
      simMetric = "pearson", numCores = 1L, JavaMemory = 4L,
      GM_jar = NULL, P2N_threshType = "off", P2N_maxMissing = 100,
      netSfx = "txt$", debugMode = FALSE)

### Arguments

`netDir` | (char) directory with .profile files
`outDir` | (char) path to directory where interaction networks are to be printed
`simMetric` | (char) similarity measure to use in converting profiles to interaction networks.
`numCores` | (integer) number of cores for parallel processing
`JavaMemory` | (integer) Memory for GeneMANIA (in Gb)
`GM_jar` | (char) path to GeneMANIA jar file
`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)
`netSfx` | (char) pattern for finding network files in `netDir`.
`debugMode` | (logical) if TRUE runs profile generation in serial rather than parallel, allowing debugging

### Details

In preparation for network integration. When using GeneMANIA's built-in functionality to create PSN using ProfileToNetworkDriver, this step needs to run to process profiles to networks. These are currently used for Pearson correlation-based networks and those using mutual information.

### Value

No value. Side effect of creating interaction networks in outDir.

[Package netDx version 1.0.3 Index]