map_orthologs_gprofiler: Map orthologs: gprofiler

In neurogenomics/orthogene: Interspecies gene mapping

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 NAs 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

neurogenomics/orthogene documentation built on Jan. 30, 2024, 4:44 a.m.