map_orthologs_custom: Map orthologs: gprofiler
In neurogenomics/orthogene: Interspecies gene mapping

map_orthologs_custom

R Documentation

Map orthologs: gprofiler

Map orthologs from one species to another using a custom gene_map table.

map_orthologs_custom(
  gene_map,
  input_species,
  output_species,
  input_col,
  output_col,
  verbose = TRUE
)

`gene_map`	A data.frame that maps the current gene names to new gene names. This function's behaviour will adapt to different situations as follows: `gene_map=<data.frame>` : When a data.frame containing the gene key:value columns (specified by `input_col` and `output_col`, respectively) is provided, this will be used to perform aggregation/expansion. `gene_map=NULL` and `input_species!=output_species` : A `gene_map` is automatically generated by map_orthologs to perform inter-species gene aggregation/expansion. `gene_map=NULL` and `input_species==output_species` : A `gene_map` is automatically generated by map_genes to perform within-species gene gene symbol standardization and aggregation/expansion.
`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.
`input_col`	Column name within `gene_map` with gene names matching the row names of `X`.
`output_col`	Column name within `gene_map` with gene names that you wish you map the row names of `X` onto.
`verbose`	Print messages.