getIdsMrna: getIdsMrna

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

getIdsMrna

Description

getIdsMrna will produce ensembl and entrez ID dataframes for mRNAs. These will be stored as 2 individual assays within a MAE.

This function will attempt to use biomaRt in the first instance. If server issues occur, it will instead use clusterProfiler. Generally biomaRt has more annotation IDs, but the results between these methods will vary.

Usage

getIdsMrna(MAE, mRNA, mirror, species, orgDB)

Arguments

MAE	MultiAssayExperiment to store the output of getIdsMrna. It is recommended to use the MAE which contains output from startObject.
mRNA	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.
mirror	String to identify which biomaRt server is best. This is based on location. Either 'useast', 'uswest', 'asia' or 'www'. Default is 'www'.
species	Species of interest. E.g. mmusculus or hsapiens.
orgDB	org.xx.eg.db package which corresponds to the species being analysed.

Value

2 new dataframes in the MAE. One with entrez information and the other with ensembl gene ID information.

Examples

library(org.Mm.eg.db)
data(mm_mRNA)

mRNA <- mm_mRNA[1:20,]

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

MAE <- getIdsMrna(MAE = MAE, mRNA = assay(MAE, 2), mirror = 'useast',
                      species = 'mmusculus', orgDB = org.Mm.eg.db)

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