eNames: eNames

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

Description

Extracts the gene IDs from nested dataframes created from the addIds function.

Usage

eNames(MAE, method = '', gene_IDs)

Arguments

MAE	MultiAssayExperiment which will store output of eNames. It is recommended to use the MAE which stores the output of addIds.
method	Either 'c' or 's', respectively for combined or separated analysis.
gene_IDs	List of DE data and associated gene IDs. This is the output from the addIds function, this should be found as metadata in the MAE used in the addIds function.

Value

A single list of entrez/ ensembl IDs for each time point. Output will be stored as metadata in the input MAE.

Examples

library(org.Mm.eg.db)

data(mm_miR)

data(mm_mRNA)

Data <- startObject(miR = mm_miR, mRNA = mm_mRNA)

Data <- getIdsMir(Data, assay(Data, 1), org.Mm.eg.db, 'mmu')

Data <- getIdsMrna(Data, assay(Data, 2), mirror = 'useast', 'mmusculus')

Data <- combineGenes(MAE = Data, miR_data = assay(Data, 1),
                     mRNA_data = assay(Data, 2))

Data <- genesList(MAE = Data, method = 'c', genetic_data = assay(Data, 9),
                  timeString = 'D')

Data <- significantVals(MAE = Data, method = 'c',
                        geneList = metadata(Data)[[1]],
                        maxVal = 0.05, stringVal = "adjPVal")

Data <- addIds(MAE = Data, method = "c",
              filtered_genelist = metadata(Data)[[2]],
              miR_IDs = assay(Data, 3), mRNA_IDs = assay(Data, 7))

Data <- eNames(MAE = Data, method = "c", gene_IDs = metadata(Data)[[3]])

TimiRGeN documentation built on April 17, 2021, 6:03 p.m.