Gene ID conversion function using biomart

Convert different gene ID types within one species or between two species using the biomart service.

Usage

GeneConvert(
  geneID,
  geneID_from_IDtype = "symbol",
  geneID_to_IDtype = "entrez_id",
  species_from = "Homo_sapiens",
  species_to = NULL,
  Ensembl_version = NULL,
  biomart = NULL,
  mirror = NULL,
  max_tries = 5,
  verbose = TRUE
)

Arguments

geneID: A vector of the geneID character.
geneID_from_IDtype: Gene ID type of the input geneID. e.g. "symbol", "ensembl_id", "entrez_id"
geneID_to_IDtype: Gene ID type(s) to convert to. e.g. "symbol", "ensembl_id", "entrez_id".
species_from: Latin names for animals of the input geneID. e.g. "Homo_sapiens", "Mus_musculus".
species_to: Latin names for animals of the output geneID. e.g. "Homo_sapiens", "Mus_musculus".
Ensembl_version: Ensembl version. NULL uses the latest.
biomart: BioMart database that you want to connect to. Possible options include "ensembl", "protists_mart", "fungi_mart", and "plants_mart".
mirror: Specify an Ensembl mirror to connect to. The valid options here are "www", "uswest", "useast", "asia".
max_tries: The maximum number of attempts to connect with the BioMart service.
verbose: Whether to print the message. Default is TRUE.

Value

A list with the following elements:

geneID_res: A data.frame contains the all gene IDs mapped in the database with columns: "from_IDtype", "from_geneID", "to_IDtype", "to_geneID".
geneID_collapse: The data.frame contains all the successfully converted gene IDs, and the output gene IDs are collapsed into a list. As a result, the "from_geneID" column (which is set as the row names) of the data.frame is unique.
geneID_expand: The data.frame contains all the successfully converted gene IDs, and the output gene IDs are expanded.
Ensembl_version: Ensembl database version.
Datasets: Datasets available in the selected BioMart database.
Attributes: Attributes available in the selected BioMart database.
geneID_unmapped: A character vector of gene IDs that are unmapped in the database.

Examples

res <- GeneConvert(
  geneID = c("CDK1", "MKI67", "TOP2A", "AURKA", "CTCF"),
  species_from = "Homo_sapiens",
  species_to = "Mus_musculus"
)
#> ℹ [2026-08-30 04:31:19] Connect to the Ensembl archives...
#> ℹ [2026-08-30 04:31:19] Using the 116 version of ensembl database...
#> ℹ [2026-08-30 04:31:19] Downloading the ensembl database from https://jun2026.archive.ensembl.org...
#> Ensembl site unresponsive, trying asia mirror
#> ℹ [2026-08-30 04:31:22] Searching the dataset hsapiens ...
#> ℹ [2026-08-30 04:31:23] Connecting to the dataset hsapiens_gene_ensembl ...
#> ℹ [2026-08-30 04:31:25] Searching the dataset mmusculus ...
#> ℹ [2026-08-30 04:31:25] Connecting to the dataset mmusculus_gene_ensembl ...
#> ℹ [2026-08-30 04:31:27] Converting the geneIDs...
#> ℹ [2026-08-30 04:31:33] 5 genes mapped with "ensembl_symbol"
#> ℹ [2026-08-30 04:31:33] ==============================
#> ℹ                       5 genes mapped
#> ℹ                       0 genes unmapped
#> ℹ                       ==============================
str(res)
#> List of 7
#>  $ geneID_res     :'data.frame':	5 obs. of  4 variables:
#>   ..$ from_IDtype: chr [1:5] "ensembl_symbol" "ensembl_symbol" "ensembl_symbol" "ensembl_symbol" ...
#>   ..$ from_geneID: chr [1:5] "CTCF" "CDK1" "TOP2A" "AURKA" ...
#>   ..$ to_IDtype  : chr [1:5] "entrez_id" "entrez_id" "entrez_id" "entrez_id" ...
#>   ..$ to_geneID  : int [1:5] 13018 12534 21973 20878 17345
#>  $ geneID_collapse:'data.frame':	5 obs. of  2 variables:
#>   ..$ from_geneID: chr [1:5] "AURKA" "CDK1" "CTCF" "MKI67" ...
#>   ..$ entrez_id  :List of 5
#>   .. ..$ : int 20878
#>   .. ..$ : int 12534
#>   .. ..$ : int 13018
#>   .. ..$ : int 17345
#>   .. ..$ : int 21973
#>   .. ..- attr(*, "class")= chr "AsIs"
#>  $ geneID_expand  :'data.frame':	5 obs. of  2 variables:
#>   ..$ from_geneID: chr [1:5] "AURKA" "CDK1" "CTCF" "MKI67" ...
#>   ..$ entrez_id  : int [1:5] 20878 12534 13018 17345 21973
#>  $ Ensembl_version: chr "116"
#>  $ Datasets       :'data.frame':	213 obs. of  3 variables:
#>   ..$ dataset    : 'AsIs' chr [1:213] "abrachyrhynchus_gene_ensembl" "acalliptera_gene_ensembl" "acarolinensis_gene_ensembl" "acchrysaetos_gene_ensembl" ...
#>   ..$ description: 'AsIs' chr [1:213] "Pink-footed goose genes (ASM259213v1)" "Eastern happy genes (fAstCal1.3)" "Green anole genes (AnoCar2.0v2)" "Golden eagle genes (bAquChr1.2)" ...
#>   ..$ version    : 'AsIs' chr [1:213] "ASM259213v1" "fAstCal1.3" "AnoCar2.0v2" "bAquChr1.2" ...
#>  $ Attributes     :'data.frame':	3175 obs. of  3 variables:
#>   ..$ name       : chr [1:3175] "ensembl_gene_id" "ensembl_gene_id_version" "ensembl_transcript_id" "ensembl_transcript_id_version" ...
#>   ..$ description: chr [1:3175] "Gene stable ID" "Gene stable ID version" "Transcript stable ID" "Transcript stable ID version" ...
#>   ..$ page       : chr [1:3175] "feature_page" "feature_page" "feature_page" "feature_page" ...
#>  $ geneID_unmapped: chr(0)

Gene ID conversion function using biomart

Usage

Arguments

Value

See also

Examples