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

(slower but more species and genes) or "homologene" (faster but fewer species and genes).

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 <- map_orthologs(
    genes = rownames(exp_mouse),
    input_species = "mouse"
)

[Package orthogene version 0.99.9 Index]