makeNet {TimiRGeN} | R Documentation

## 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)

[Package TimiRGeN version 1.4.0 Index]