multiReg {TimiRGeN} | R Documentation |
Creates a new matrix containing the gene of interest and each binding partner that it interacts with.
multiReg(MAE, gene_interest, mRNAreg, filt_df, miRNA_exp, mRNA_exp)
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 |
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.
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]])