getIdsMrna: getIdsMrna

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

Description

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

Usage

getIdsMrna(MAE, mRNA, mirror, species)

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.

Value

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

Examples

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')

TimiRGeN documentation built on April 17, 2021, 6:03 p.m.