WriteExplainedNodesToSifFile: Write explained nodes to Sif file

In CausalR: Causal network analysis methods

Description

Outputs networks of explained nodes in .sif file format for producing visualisations using Cytoscape. Output will be to a directory beginning with a timestamp,

Usage

WriteExplainedNodesToSifFile(hypothesisnode, signOfHypothesis, network,
  experimentalData, delta, outputDir = getwd(), outputFilesName = "",
  correctlyExplainedOnly = FALSE, quiet = FALSE)

Arguments

hypothesisnode	a hypothesis node
signOfHypothesis	the direction of change of hypothesis node
network	a computational causal graph
experimentalData	The experimental data read in using ReadExperimentalData. The results is an n x 2 matrix; where the first column contains the node ids of the nodes in the network that the results refer to. The second column contains values indicating the direction of regulation in the results - (+)1 for up, -1 for down and 0 for insignificant amounts of regulation. The name of the first column is the filename the data was read from.
delta	the number of edges across which the hypothesis should be followed
outputDir	the directory to output the files to. Default is the working directory
outputFilesName	a character string to use for the name of the output files. Default value is "", which results in files using the default naming convention of "network file name-data file name-delta value-node name". Set to NA if not writing to file.
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

hypothesisnode <- "Node0"
signOfHypothesis <- +1
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
WriteExplainedNodesToSifFile(hypothesisnode, signOfHypothesis, network, experimentalData, delta,
                             outputFilesName=NA)

CausalR documentation built on Nov. 8, 2020, 5:25 p.m.