Map genes — map_genes • orthogene

Input a list of genes, transcripts, proteins, SNPs, or genomic ranges in any format (HGNC, Ensembl, RefSeq, UniProt, etc.) and return a table with standardised gene symbols (the "names" column).

map_genes(
  genes,
  species = "hsapiens",
  target = "ENSG",
  mthreshold = Inf,
  drop_na = FALSE,
  numeric_ns = "",
  run_map_species = TRUE,
  verbose = TRUE
)

Arguments

genes: Gene list.
species: Species to map against.
target: target namespace.
mthreshold: maximum number of results per initial alias to show. Shows all by default.
drop_na: Drop all genes without mappings. Sets gprofiler2::gconvert(filter_na=) as well an additional round of more comprehensive NA filtering by orthogene.
numeric_ns: namespace to use for fully numeric IDs (list of available namespaces).
run_map_species: Standardise species names with map_species first (Default: TRUE).
verbose: Print messages.

Value

Table with standardised genes.

Details

Uses gconvert. The exact contents of the output table will depend on target parameter. See ?gprofiler2::gconvert for more details.

Examples

genes <- c(
    "Klf4", "Sox2", "TSPAN12", "NM_173007", "Q8BKT6",
    "ENSMUSG00000012396", "ENSMUSG00000074637"
)
mapped_genes <- map_genes(
    genes = genes,
    species = "mouse"
)
#> Retrieving all organisms available in gprofiler.
#> Using stored `gprofiler_orgs`.
#> Mapping species name: mouse
#> Common name mapping found for mouse
#> 1 organism identified from search: mmusculus
#> 7 / 7 (100%) genes mapped.