addIds {TimiRGeN} | R Documentation |
Adds entrez or ensembl IDs to the nested dataframes within a list(c) or list of lists (s). The IDs are created by the getIdsMir and getIdsMrna functions, both are needed for addIds.
addIds(MAE, method, filtered_genelist, miR_IDs, mRNA_IDs)
MAE |
MultiAssayExperiment to store the output of addIds. It is recommended to use the MAE which stores results from significantVals. |
method |
Either "c" or "s", respectively for combined or separated analysis. |
filtered_genelist |
A list of nested dataframes if 'c' or a list of lists with nested dataframes if 's'. This will be found as metadata within the MAE object used in the significantVals function. |
miR_IDs |
miR_ensembl or miR_entrez. Use a getIDsMir function to acquire this. This will be stored as an assay in the MAE used in a getIdsMir function. |
mRNA_IDs |
mRNA_ensembl or mRNA_entrez. Use a getIDsMrna function to acquire this. This will be stored as an assay in the MAE used in a getIdsMrna function. |
List of dataframes with entrezIDs/ ensembl IDs and gene names as columns which 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), orgDB = org.Mm.eg.db, 'mmu') Data <- getIdsMrna(Data, assay(Data, 2), mirror = 'useast', species = 'mmusculus', orgDB = 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))