makeNet {TimiRGeN} | R Documentation |
Creates an igraph object from filtered miR-mRNA interactions. Resulting list can be used to display an internal R miR-mRNA interaction network.
makeNet(MAE, filt_df)
MAE |
MultiAssayExperiment to store output from makeNet. It is recommended to use the same MAE which stores output from matrixFilter. |
filt_df |
Filtered miR-mRNA interactions produced by the matrixFilter function. This should be stored as an assay within the MAE used in the matrixFilter function. |
A list of igraph data which represent miR-mRNA interactions filtered from the input data, wikipathway of choice and database mining, This list is input for quickNet. Output will be stored as metadata in the input MAE.
Filt_df <- data.frame(row.names = c("mmu-miR-320-3p:Acss1", "mmu-miR-27a-3p:Odc1"), corr = 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)) MAE <- MultiAssayExperiment() MAE <- makeNet(MAE, Filt_df)