Gene ID conversion function using biomart

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 = 103,
  biomart = NULL,
  mirror = NULL,
  max_tries = 5
)

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.

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"),
  geneID_from_IDtype = "symbol",
  geneID_to_IDtype = "entrez_id",
  species_from = "Homo_sapiens",
  species_to = "Mus_musculus",
  Ensembl_version = 103
)
#> Connect to the Ensembl archives...
#> Using the 103 version of biomart...
#> Connecting to the biomart...
#> Searching the dataset hsapiens ...
#> Connecting to the dataset hsapiens_gene_ensembl ...
#> Searching the dataset mmusculus ...
#> Connecting to the dataset mmusculus_gene_ensembl ...
#> Converting the geneIDs...
#> Error in collect(., Inf): Failed to collect lazy table.
#> Caused by error in `db_collect()`:
#> ! Arguments in `...` must be used.
#> ✖ Problematic argument:
#> • ..1 = Inf
#> ℹ Did you misspell an argument name?
str(res)
#> Error in eval(expr, envir, enclos): object 'res' not found

# Convert the human genes to mouse homologs and replace the raw counts in a Seurat object.
data("pancreas_sub")
counts <- pancreas_sub@assays$RNA@counts
res <- GeneConvert(
  geneID = rownames(counts),
  geneID_from_IDtype = "symbol",
  geneID_to_IDtype = "symbol",
  species_from = "Mus_musculus",
  species_to = "Homo_sapiens",
  Ensembl_version = 103
)
#> Connect to the Ensembl archives...
#> Using the 103 version of biomart...
#> Connecting to the biomart...
#> Searching the dataset mmusculus ...
#> Connecting to the dataset mmusculus_gene_ensembl ...
#> Converting the geneIDs...
#> Error in collect(., Inf): Failed to collect lazy table.
#> Caused by error in `db_collect()`:
#> ! Arguments in `...` must be used.
#> ✖ Problematic argument:
#> • ..1 = Inf
#> ℹ Did you misspell an argument name?
# Check the number of input and converted gene IDs
input_genes <- length(rownames(counts))
db_genes <- length(unique(res$geneID_res$from_geneID))
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'unique': object 'res' not found
converted_genes_input <- length(unique(res$geneID_collapse$from_geneID))
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'unique': object 'res' not found
converted_genes_output <- length(unique(res$geneID_expand$symbol))
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'unique': object 'res' not found
cat("Number of input gene IDs:", input_genes, "\n")
#> Number of input gene IDs: 15958 
cat("Number of gene IDs mapped in the database:", db_genes, "\n")
#> Error in eval(expr, envir, enclos): object 'db_genes' not found
cat("Number of input gene IDs that were successfully converted:", converted_genes_input, "\n")
#> Error in eval(expr, envir, enclos): object 'converted_genes_input' not found
cat("Number of converted gene IDs:", converted_genes_output, "\n")
#> Error in eval(expr, envir, enclos): object 'converted_genes_output' not found

homologs_counts <- aggregate(
  x = counts[res$geneID_expand[, "from_geneID"], ],
  by = list(res$geneID_expand[, "symbol"]), FUN = sum
)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'aggregate': error in evaluating the argument 'i' in selecting a method for function '[': object 'res' not found
rownames(homologs_counts) <- homologs_counts[, 1]
#> Error in eval(expr, envir, enclos): object 'homologs_counts' not found
homologs_counts <- as(as_matrix(homologs_counts[, -1]), "dgCMatrix")
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'as.matrix': object 'homologs_counts' not found
homologs_counts
#> Error in eval(expr, envir, enclos): object 'homologs_counts' not found