cytoMake {TimiRGeN} | R Documentation |
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.
cytoMake(interactionData, titleString = '', collectionString = '')
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". |
A network of filtered miR-mRNA interactions specific for a pathway of interest. It will be visible in cytoscape version 3.7 or later.
## 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)