getIdsMrna {TimiRGeN} | R Documentation

## 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)

[Package TimiRGeN version 1.2.0 Index]