eNames {TimiRGeN} | R Documentation |
Extracts the gene IDs from nested dataframes created from the addIds function.
eNames(MAE, method = '', gene_IDs)
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. |
A single list of entrez/ ensembl IDs for each time point. Output will be stored as metadata in the input MAE.
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]])