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]