findpaths.simple | R Documentation |
Identify signaling pathway source and target genes (cell surface receptors and transcriptional regulators, specifically) in the weighted protein interaction network. Create a .sh file and run it using the terminal to call the java code in Flow.jar. The computations are stored in the specified directories and can be read using the summarize function. The java code is written in the CellCommJava folder in the package directory. The java folder in the package directory has the code with some modifications to be used in the findpaths.simpleRJava function.
findpaths.simple(sources.targets, file, dir, maindir) ## S4 method for signature 'CellComm' findpaths.simple(sources.targets, file, dir, maindir)
sources.targets |
list; the sources and targets of the interaction
receptor as calculated by the sourcestargets function:
|
file |
character; the .txt file corresponding to the cell population. ? |
dir |
character; directory for the selected interaction. |
maindir |
character; directory where the directories for each interaction will be saved. |
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