convertProfileToNetworks: Convert profiles to interaction networks before integration

In BaderLab/netDx: Network-based patient classifier

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.

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