convertProfileToNetworks {netDx} | R Documentation |
Convert profiles to interaction networks before integration
convertProfileToNetworks(netDir, outDir = tempdir(), simMetric = "pearson", numCores = 1L, JavaMemory = 4L, GM_jar = NULL, P2N_threshType = "off", P2N_maxMissing = 100, netSfx = "txt$", debugMode = FALSE)
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 |
debugMode |
(logical) if TRUE runs profile generation in serial rather than parallel, allowing debugging |
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.
No value. Side effect of creating interaction networks in outDir.