getIdsMir: getIdsMir

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

getIdsMir

Description

getIdsMir will produce ensembl and entrez ID data for microRNAs. It will also produce adjusted ensembl and entrez for IDs that are specific to microRNAs that share an ID. They will be stored as 4 individual assays in a MAE. org.Mm.eg.db must be loaded prior to using this function.

Usage

getIdsMir(MAE, miR, orgDB, miRPrefix)

Arguments

MAE	MultiAssayExperiment to store the output of getIdsMir. It is recommended to use the MAE which contains output from startObject.
miR	A Dataframe. Rownames are genes and columns are results of DE. This should be found as an assay within the MAE used in the startObject function. Please read vignette for nomenclature guidance.
orgDB	org.xx.eg.db package which corresponds to the species being analysed.
miRPrefix	microRNA prefix for the species being analysed e.g. 'mmu', 'hsa', 'rno' ect.

Value

4 dataframes consisting of either entrez or ensembl ID information. 2 of these will be adjusted for shared IDs. Output will be stored as assays in the input MAE.

Examples

library(org.Mm.eg.db)

data(mm_miR)

# Make sure miRNA gene name nomenclature is correct for TimiRGeN analysis!

miR <- mm_miR[1:100,]

MAE <- startObject(miR = miR, mRNA = NULL)

MAE <- getIdsMir(MAE, assay(MAE, 1), orgDB = org.Mm.eg.db, miRPrefix = 'mmu')

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