map_orthologs_babelgene: Map orthologs: babelgene

In neurogenomics/orthogene: Interspecies gene mapping

Map orthologs: babelgene

Description

Map orthologs from one species to another using orthologs.

Usage

map_orthologs_babelgene(
  genes,
  input_species,
  output_species = "human",
  min_support = 1,
  top = FALSE,
  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.
min_support	Minimum number of supporting source databases. Gene pairs available in this package are supported by 2 to 12 databases (the maximum varies depending on the species).
top	For each gene, output only the match with the highest support level if there are multiple hits.
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.

Value

Ortholog map data.frame

Source

babelgene tutorial

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