loadCircuit: Load the topology from a file.

In TheJacksonLaboratory/sRACIPE_dev: Systems biology tool to simulate gene regulatory circuits

Description

Read an input file and return the circuit information as a list. A typical topology file looks like

Source	Target	Type
geneA	geneB	2
geneB	geneC	1
geneB	geneA	2

Here the regulation type is specified by number - activation: 1, inhibition: 2

Usage

loadCircuit(circuit = "inputs/test.tpo", header = TRUE)

Arguments

circuit	Character or data.frame. Topology file address or as a data.frame.
header	(optional) Logical. Whether the input file has a header or not. TRUE by default.

Value

List. Contains the number of genes, circuit name, topology (Source, Target, Type), and directory path.

Related Functions

simulateGRC, knockdownAnalysis, overExprAnalysis, plotData, calcHeatmapSimilarity

Examples

topologyInfo <- loadCircuit("inputs/test.tpo")

TheJacksonLaboratory/sRACIPE_dev documentation built on May 7, 2019, 8:16 a.m.