Skip to contents

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

An integer specifying the Ensembl version. Default is NULL. If NULL, the latest version will be used.

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.

See also

AnnotateFeatures

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]
} # }