quickNet: quickNet

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

quickNet

Description

Generates an igraph network representing the miR-mRNA interactions filtered from the input data using pathway analysis and database filtering. Pink nodes are miRs and light blue nodes are mRNAs. Edges are coloured by the average correlations. Note, plot window size may need to be adjusted to accommodate image.

Usage

quickNet(net, pathwayname)

Arguments

net	List generated by makeNet function. If you have fewer than two interactions the plot will not work. Output from makeNet should be stored as metadata within the MAE used in the makeNet function.
pathwayname	Character which is the name of pathway of interest. Default is "Pathway".

Value

A network depicting filtered miR-mRNA interactions for a specific wikipathway of interest.

Examples

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)

quickNet(metadata(MAE)[[1]])

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