map_orthologs {orthogene} | R Documentation |
Map orthologs from one species to another.
map_orthologs( genes, standardise_genes = FALSE, input_species, output_species = "human", method = c("gprofiler", "homologene"), mthreshold = Inf, verbose = TRUE, ... )
genes |
can be a mixture of any format (HGNC, Ensembl, RefSeq, UniProt, etc.) and will be automatically converted to standardised HGNC symbol format. |
standardise_genes |
If |
input_species |
Name of the input species (e.g., "mouse","fly"). Use map_species to return a full list of available species. |
output_species |
Name of the output species (e.g. "human","chicken"). Use map_species to return a full list of available species. |
method |
R package to to use for gene mapping:
|
mthreshold |
Maximum number of ortholog names per gene to show.
Passed to gorth.
Only used when |
verbose |
Print messages. |
... |
Additional arguments to be passed to
gorth or homologene. |
map_orthologs()
is a core function within
convert_orthologs()
, but does not have many
of the extra checks, such as non121_strategy
)
and drop_nonorths
.
Ortholog map data.frame
with at
least the columns "input_gene" and "ortholog_gene".
data("exp_mouse") gene_map <- orthogene::map_orthologs( genes = rownames(exp_mouse), input_species = "mouse" )