WriteAllExplainedNodesToSifFile {CausalR} | R Documentation |
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.
WriteAllExplainedNodesToSifFile(scanResults, network, experimentalData, delta, correctlyExplainedOnly = TRUE, quiet = TRUE)
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. |
files containing paths from hypothesis node to explained nodes in sif format and corresponding annotation (_anno.txt) files
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)