makeNet: makeNet

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

makeNet

Description

Creates an igraph object from filtered miR-mRNA interactions. Resulting list can be used to display an internal R miR-mRNA interaction network.

Usage

makeNet(MAE, filt_df)

Arguments

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.

Value

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.

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)

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