multiReg {TimiRGeN} | R Documentation

## multiReg

### Description

Creates a new matrix containing the gene of interest and each binding partner that it interacts with.

### Usage

    multiReg(MAE, gene_interest, mRNAreg, filt_df, miRNA_exp, mRNA_exp)

### Arguments

`MAE` | Input MAE which stores results from multiReg It is recommended to use the MAE which was used in matrixFilter.
`gene_interest` | Name of gene of interest. Full string required with no spelling mistakes e.g. "mmu-miR-140-5p", "Ffg1", "hsa-miR-29a-5p". If gene of interest is an mRNA, mRNAreg must be TRUE. Otherwise, if the gene of interest is a miRNA, then mRNAreg must be FALSE.
`mRNAreg` | TRUE or FALSE. Is the gene of interest a mRNA? Default is TRUE.
`filt_df` | Dataframe from the matrixFilter function.
`miRNA_exp` | miRNA data from using the diffExpressRes function on miRNA data.
`mRNA_exp` | mRNA data from using the diffExpressRes function on miRNA data

### Value

A matrix which contains the gene of interest and all binding partners. Their values (Log2FC or ave exp) for each time point are also produced.

### Examples

    library(org.Mm.eg.db)

    miR <- mm_miR[1:100,]

    mRNA <- mm_mRNA[1:200,]

    MAE <- startObject(miR = miR, mRNA = mRNA)

    MAE <- getIdsMir(MAE, assay(MAE, 1), orgDB = org.Mm.eg.db, 'mmu')

    MAE <- getIdsMrna(MAE, assay(MAE, 2), "useast", 'mmusculus', )

    MAE <- diffExpressRes(MAE, df = assay(MAE, 1), dataType = 'Log2FC',
                         genes_ID = assay(MAE, 3),
                          idColumn = 'GENENAME',
                          name = "miRNA_log2fc")

    MAE <- diffExpressRes(MAE, df = assay(MAE, 2), dataType = 'Log2FC',
                         genes_ID = assay(MAE, 7),
                         idColumn = 'GENENAME',
                         name = "mRNA_log2fc")

    Filt_df <- data.frame(row.names = c("mmu-miR-145a-3p:Adamts15",
                                       "mmu-miR-146a-5p:Acy1"),
                         corr = c(-0.9191653, 0.7826041),
                         miR = c("mmu-miR-145a-3p", "mmu-miR-146a-5p"),
                         mRNA = c("Adamts15", "Acy1"),
                         miR_Entrez = c(387163, NA),
                         mRNA_Entrez = c(235130, 109652),
                         TargetScan = c(1, 0),
                         miRDB = c(0, 0),
                         Predicted_Interactions = c(1, 0),
                         miRTarBase = c(0, 1),
                         Pred_Fun = c(1, 1))

    MAE <- matrixFilter(MAE, miningMatrix = Filt_df, negativeOnly = FALSE,
                       threshold = 1, predictedOnly = FALSE)

    MAE <- multiReg(MAE = MAE, gene_interest = "Adamts15",
                    mRNAreg =TRUE, filt_df=MAE[[11]], miRNA_exp=MAE[[9]],
                    mRNA_exp=MAE[[10]])

[Package TimiRGeN version 1.4.0 Index]