Get Species Pathways

Retrieves pathway information for a specific species and optionally filters for specific genes.

Usage

get_pathways(species_id, genes = NULL, category = "GOBP")

Arguments

species_id

Numeric. The ID of the desired species (e.g., from srch_species).

genes

A vector or column of a data frame containing gene IDs of interest. If NULL (default), returns all pathways for the species.

category

Character. A vector or character constant of pathway categories/databases (e.g. KEGG, GOBP, GOCC, etc.). It is not recommended to use all categories, as some species have many, leading to performance issues

Value

A data frame containing pathway information. If genes are provided, the data frame is filtered to include only pathways containing those genes and joined with gene mapping data.

Details

The function first retrieves the pathway and pathwayInfo tables for the specified species. If a list of genes is provided, it converts the IDs to Ensembl IDs, matches them against the pathway map, and joins the results with pathway metadata.