map_genes {orthogene} | R Documentation |
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 = "", verbose = TRUE )
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 |
numeric_ns |
namespace to use for fully numeric IDs (list of available namespaces). |
verbose |
Print messages. |
Uses gconvert.
The exact contents of the output table will depend on
target
parameter.
See ?gprofiler2::gconvert
for more details.
Table with standardised genes.
genes <- c( "Klf4", "Sox2", "TSPAN12", "NM_173007", "Q8BKT6", "ENSMUSG00000012396", "ENSMUSG00000074637" ) mapped_genes <- map_genes( genes = genes, species = "mouse" )