eNames {TimiRGeN} | R Documentation

## eNames

### 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)

    miR <- mm_miR[1:50,]

    mRNA <- mm_mRNA[1:100,]

    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', org.Mm.eg.db)

    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]])

[Package TimiRGeN version 1.2.0 Index]