findpaths.simple-methods: Identify trajectories connecting populations in the...

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

Identify trajectories connecting populations in the interaction.

Description

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.

Usage

findpaths.simple(sources.targets, file, dir, maindir)

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

Arguments

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.