WriteAllExplainedNodesToSifFile: Write all explained nodes to Sif file

Description Usage Arguments Value Examples

View source: R/WriteAllExplainedNodesToSifFile.r

Description

Outputs networks of all explained nodes in .sif file format, named by node name with sign of regulation, each with a corresponding annotation file for producing visualisations using Cytoscape.

Usage

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WriteAllExplainedNodesToSifFile(scanResults, network, experimentalData, delta,
  correctlyExplainedOnly = TRUE, quiet = TRUE)

Arguments

scanResults

a results object produced by ScanR

network

a computational causal graph

experimentalData

The experimental data read in using ReadExperimentalData.

delta

the number of edges across which the hypothesis should be followed, the setting should be that used to generate the input ScanR object.

correctlyExplainedOnly

if TRUE network files will only be produced for correctly explained nodes. If FALSE network files will be produced for each of correctly explained, incorrectly explained and ambiguously explained nodes.

quiet

a flag to suppress output to console. FALSE by default.

Value

files containing paths from hypothesis node to explained nodes in sif format and corresponding annotation (_anno.txt) files

Examples

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networkFile <- system.file(package='CausalR', 'extdata', 'testNetwork1.sif')
network <- CreateCCG(networkFile)
experimentalDataFile <- system.file(package='CausalR', 'extdata', 'testData1.txt')
experimentalData <- ReadExperimentalData(experimentalDataFile, network)
delta <- 2
scanResults <- runSCANR(network, experimentalData, numberOfDeltaToScan = delta,
    topNumGenes = 2, writeResultFiles = FALSE, writeNetworkFiles = "none",
    quiet = FALSE, doParallel = TRUE, numCores = 2)
WriteAllExplainedNodesToSifFile(scanResults, network, experimentalData, delta,
    correctlyExplainedOnly = TRUE, quiet = TRUE)

CausalR documentation built on Nov. 1, 2018, 2:12 a.m.