gmtEnsembl {TimiRGeN} | R Documentation

## gmtEnsembl

### Description

Change entrez IDs in path_gene and path_data into ensembl IDs. Will create two new dataframes with ensembl IDs and wikipathway information.

### Usage

    gmtEnsembl(MAE, path_gene, path_data, orgDB)

### Arguments

`MAE` | MultiAssayExperiment which will store the output of gmtEnsembl. It is recommended to use the same MAE object which contains output from dloadGmt.
`path_gene` | Dataframe with wikipathway IDs and entrezgene IDs. path_gene is from the dloadGmt function. It will be stored as an assay within the MAE used in the dloadGmt function.
`path_data` | Dataframe with wikipathway IDs, wikipathway names and entrezgene IDs. path_data is from the dloadGmt function. It will be stored as an assay within the MAE used in the dloadGmt function.
`orgDB` | Load the appropriate db package e.g. org.Hs.eg.db if human wikipathways are being used.

### Value

2 dataframes. One containing wikipathway IDs and ensembl gene IDs, and the other containing wikipathway IDs, ensembl gene IDs and wikipathway names. Output will be stored as assays in the input MAE.

### Examples

    library(org.Mm.eg.db)

    miR <- mm_miR[1:50,]

    mRNA <- mm_mRNA[1:100,]

    MAE <- startObject(miR = mm_miR, mRNA = mm_mRNA)

    MAE <- dloadGmt(MAE, species = "Mus musculus")

    MAE <- gmtEnsembl(MAE = MAE, assay(MAE, 3),
                       assay(MAE, 5), org.Mm.eg.db)

[Package TimiRGeN version 1.2.0 Index]