convertProfileToNetworks: Convert profiles to interaction networks before integration

Description Usage Arguments Details Value

View source: R/runProfileToNetworks.R

Description

Convert profiles to interaction networks before integration

Usage

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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.


netDx documentation built on Dec. 11, 2020, 2:01 a.m.