convertGeneIDs {singleCellTK} | R Documentation

## Convert Gene IDs

### Description

Convert the gene IDs in a SingleCellExperiment object using Bioconductor org.*.eg.db data packages. Because annotation databases do not have a 1:1 relationship, this tool removes rows with no corresponding annotation in your desired annotation, and remove any duplicate annotations after conversion.

### Usage

    convertGeneIDs(inSCE, inSymbol, outSymbol, database = "org.Hs.eg.db")

### Arguments

`inSCE` | Input SingleCellExperiment object.
`inSymbol` | The input symbol type
`outSymbol` | The output symbol type
`database` | The org.*.eg.db database to use. The default is org.Hs.eg.db

### Value

A SingleCellExperiment object with converted gene IDs.

### Examples

    if(requireNamespace("org.Mm.eg.db", quietly = TRUE)) {
      #convert mouse gene symbols to ensembl IDs
      library("org.Mm.eg.db")
      sample(rownames(mouseBrainSubsetSCE), 50)
      mouseBrainSubsetSymbol <- convertGeneIDs(inSCE = mouseBrainSubsetSCE,
                                               inSymbol = "SYMBOL",
                                               outSymbol = "ENSEMBL",
                                               database = "org.Mm.eg.db")
      sample(rownames(mouseBrainSubsetSymbol), 50)
    }

[Package singleCellTK version 2.2.0 Index]