map_orthologs_gprofiler {orthogene} | R Documentation

## Map orthologs: gprofiler

### Description

Map orthologs from one species to another using gorth.

### Usage

    map_orthologs_gprofiler(
      genes,
      input_species,
      output_species = "human",
      filter_na = FALSE,
      mthreshold = Inf,
      verbose = TRUE,
      ...
    )

### Arguments

`genes` | Gene list.
`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.
`filter_na` | Logical indicating whether to filter out results without a corresponding target name. (DEFAULT is `FALSE`, so that `NA`s can be handled by orthogene).
`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.

### Details

"`mthreshold` is used to set the maximum number of ortholog names per gene to show. This is useful to handle the problem of having many orthologs per gene (most of them uninformative). The function tries to find the most informative by selecting the most popular ones."
~ From `gprofiler2` vignette

Available namespaces for the `numeric_ns` argument can be found here.

### Value

Ortholog map `data.frame`

[Package orthogene version 1.0.2 Index]