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Gene ID conversion function using biomart

Source: R/GeneConvert.R
GeneConvert.Rd

This function can 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 database version. If NULL, use the current release version.

biomart

The name of the 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

if (FALSE) { # \dontrun{
res <- GeneConvert(
  geneID = c("CDK1", "MKI67", "TOP2A", "AURKA", "CTCF"),
  species_from = "Homo_sapiens",
  species_to = "Mus_musculus"
)
str(res)

# Convert the human genes to mouse homologs,
# and replace the raw counts in a Seurat object.
data(pancreas_sub)
counts <- GetAssayData5(
  pancreas_sub,
  assay = "RNA",
  layer = "counts"
)
res <- GeneConvert(
  geneID = rownames(counts),
  geneID_from_IDtype = "symbol",
  geneID_to_IDtype = "symbol",
  species_from = "Mus_musculus",
  species_to = "Homo_sapiens"
)

homologs_counts <- stats::aggregate(
  x = counts[res$geneID_expand[, "from_geneID"], ],
  by = list(res$geneID_expand[, "symbol"]), FUN = sum
)
rownames(homologs_counts) <- homologs_counts[, 1]
homologs_counts <- methods::as(
  thisutils::as_matrix(homologs_counts[, -1]),
  "dgCMatrix"
)
homologs_counts[1:5, 1:5]
} # }