makeDynamic: makeDynamic

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

makeDynamic

Description

Produces a dataframe that can be imported into pathvisio to show how changes in genes expression levels over the time course. Follow instructions found in the vignette which show how to save this file and further instructions found in the issues section of the TimiRGeN gihub https://github.com/Krutik6/TimiRGeN/issues/2.

Usage

makeDynamic(MAE, miR_expression, mRNA_expression, miR_IDs_adj,
                   dataType = '')

Arguments

MAE	MultiAssayExpreriment to store the output of makeDynamic. It is recommended to use the same MAE which stores output from matrixFilter.
miR_expression	Dataframe containing abundance values (e.g. log2fc or average expression) from miR specific differential expression , along with gene IDs. This is the output from diffExpressRes. Output of diffExpressRes should be stored as an assay within the MAE used in diffExpressRes.
mRNA_expression	Dataframe containing abundance values (log2fc or average expression) from mRNA specific differential expression, along with gene IDs. This is the output from diffExpressRes. Output of diffExpressRes should be stored as an assay within the MAE used in diffExpressRes.
miR_IDs_adj	Dataframe which contains adjusted gene IDs from miR data. Either miR_adjusted_entrez or miR_adjusted_ensembl. Should be found as an assay in the MAE used a getIdsMir function.
dataType	String which represents the gene ID used in this analysis. Either "En" (ensembl data) or "L" (entrez data).

Value

miR and mRNA dynamic data that can be saved and be used in pathvisio to display dynamic behaviour of miRs and mRNAs of interest over the time series in a signalling pathway of interest. Output will be stored as an assay in the input MAE.

Examples

library(org.Mm.eg.db)

miR <- mm_miR[1:50,]

mRNA <- mm_mRNA[1:100,]

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', orgDB = org.Mm.eg.db)

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

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

MAE <- makeDynamic(MAE, miR_expression = assay(MAE, 9),
                  mRNA_expression = assay(MAE, 10),
                  miR_IDs_adj = assay(MAE, 5),
                  dataType = "L")

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