cytoMake {TimiRGeN} | R Documentation

## 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)

[Package TimiRGeN version 1.4.0 Index]