map_orthologs {orthogene}R Documentation

Map orthologs

Description

Map orthologs from one species to another.

Usage

map_orthologs(
  genes,
  standardise_genes = FALSE,
  input_species,
  output_species = "human",
  method = c("gprofiler", "homologene"),
  mthreshold = Inf,
  verbose = TRUE,
  ...
)

Arguments

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 TRUE AND gene_output="columns", a new column "input_gene_standard" will be added to gene_df containing standardised HGNC symbols identified by gorth.

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:

  • "gprofiler" : Slower but more species and genes.

  • "homologene" : Faster but fewer species and genes.

  • "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.

mthreshold

Maximum number of ortholog names per gene to show. Passed to gorth. Only used when method="gprofiler" (DEFAULT : Inf).

verbose

Print messages.

...

Additional arguments to be passed to gorth or homologene.

NOTE: To return only the most "popular" interspecies ortholog mappings, supply mthreshold=1 here AND set method="gprofiler" above. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs.

For more details, please see here.

Details

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.

Value

Ortholog map data.frame with at least the columns "input_gene" and "ortholog_gene".

Examples

data("exp_mouse")
gene_map <- orthogene::map_orthologs(
    genes = rownames(exp_mouse),
    input_species = "mouse"
)

[Package orthogene version 1.0.2 Index]