cytoMake: cytoMake

In Krutik6/TimiRGeN: Time sensitive microRNA-mRNA integration, analysis and network generation tool

cytoMake

Description

Creates a cytoscape network based on the output of matrixFilter. Requires cytoscapePing() to be used. Make sure Cytoscape is open first. Must use Cytoscape version 3.7 or later.

Usage

cytoMake(interactionData, titleString = '', collectionString = '')

Arguments

interactionData	Dataframe which contains filtered miR-mRNA interactions. This is output from matrixFilter and should be found as an assay within the MAE used in the matrixFilter function.
titleString	Title of the network. Enter a string which cytoscape will see as the graph name. Default is "Network".
collectionString	Title of the collection of networks. Enter string which cytoscape will see as the collection name. Many differently titled graphs can be added to a single collection. Default is "miR-mRNA interactions".

Value

A network of filtered miR-mRNA interactions specific for a pathway of interest. It will be visible in cytoscape version 3.7 or later.

Examples

## Not run: 
Filt_df <- data.frame(row.names = c("mmu-miR-320-3p:Acss1",
                                    "mmu-miR-27a-3p:Odc1"),
                      avecor = c(-0.9191653, 0.7826041),
                      miR = c("mmu-miR-320-3p", "mmu-miR-27a-3p"),
                      mRNA = c("Acss1", "Acss1"),
                      miR_Entrez = c(NA, NA),
                      mRNA_Entrez = c(68738, 18263),
                      TargetScan = c(1, 0),
                      miRDB = c(0, 0),
                      Predicted_Interactions = c(1, 0),
                      miRTarBase = c(0, 1),
                      Pred_Fun = c(1, 1))

RCy3::cytoscapePing()

cytoMake(interactionData = Filt_df, titleString = 'test' ,
         collectionString = 'collectiontest')

## End(Not run)

Krutik6/TimiRGeN documentation built on Jan. 27, 2024, 7:46 p.m.