Convert Gene IDs

Source: R/convertGeneIDs.R

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.

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)
}

#> 
#> Loading required package: AnnotationDbi
#> 'select()' returned 1:many mapping between keys and columns
#> 127 ENSEMBL are NA after conversion. Removing
#> 29 SYMBOL are duplicated after conversion. Removing additional copies
#> 2314 SYMBOL originally, 2187 ENSEMBLs
#>  [1] "ENSMUSG00000028797" "ENSMUSG00000066129" "ENSMUSG00000002102"
#>  [4] "ENSMUSG00000027087" "ENSMUSG00000024194" "ENSMUSG00000006005"
#>  [7] "ENSMUSG00000030726" "ENSMUSG00000021796" "ENSMUSG00000028790"
#> [10] "ENSMUSG00000031812" "ENSMUSG00000026509" "ENSMUSG00000062234"
#> [13] "ENSMUSG00000030663" "ENSMUSG00000024952" "ENSMUSG00000057134"
#> [16] "ENSMUSG00000022404" "ENSMUSG00000091803" "ENSMUSG00000026675"
#> [19] "ENSMUSG00000003534" "ENSMUSG00000006800" "ENSMUSG00000024853"
#> [22] "ENSMUSG00000041685" "ENSMUSG00000026833" "ENSMUSG00000020431"
#> [25] "ENSMUSG00000073676" "ENSMUSG00000057236" "ENSMUSG00000000581"
#> [28] "ENSMUSG00000013236" "ENSMUSG00000005125" "ENSMUSG00000107722"
#> [31] "ENSMUSG00000032637" "ENSMUSG00000059119" "ENSMUSG00000021670"
#> [34] "ENSMUSG00000026421" "ENSMUSG00000052698" "ENSMUSG00000053119"
#> [37] "ENSMUSG00000038936" "ENSMUSG00000010277" "ENSMUSG00000059173"
#> [40] "ENSMUSG00000039716" "ENSMUSG00000019528" "ENSMUSG00000031342"
#> [43] "ENSMUSG00000028795" "ENSMUSG00000037608" "ENSMUSG00000022427"
#> [46] "ENSMUSG00000000326" "ENSMUSG00000035649" "ENSMUSG00000071866"
#> [49] "ENSMUSG00000027457" "ENSMUSG00000027523"