findpaths.simpleRJava-methods: Identify signaling pathways connecting cell surface receptors...

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Identify signaling pathways connecting cell surface receptors to transcriptional regulators in the protein-protein interaction network.

Description

Identify trajectories surface receptors to transcriptional regulators in the protein-protein interaction network. The code uses the rJava library and does not write and run a .sh file as the findpaths.simple function does. The java code saves the data in files which address is stored in assay@sampTab. These files will be processed by the processTrajectories function. This function uses the java code stored in the java folder in the package directory. If you are a linux user and the rJava library is not installed, please check the topic at https://stackoverflow.com/questions/12872699/error-unable-to-load-installed-packages-just-now.

Usage

findpaths.simpleRJava(object, sources.targets, file, dir, maindir)

## S4 method for signature 'CellComm'
findpaths.simpleRJava(object, sources.targets, file, dir, maindir)

Arguments

object	CellComm object.
sources.targets	list; the sources and targets of the interaction receptor as calculated by the sourcestargets function: sts[['receptor']][[interaction]].
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.

Value

Message indicating conclusion.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.