Filter Pathway Information By Category — path

Retrieves pathway mapping information for a specific species, filtered by one or more pathway categories (e.g., "GOBP", "KEGG"). Optionally, the results can be further restricted to a specific list of genes.

Usage

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

Arguments

species_id: Numeric. The ID of the species to search for.
genes: Character vector (optional). A vector of gene IDs to filter the pathways. If NULL (default), pathways for all genes in the category are returned.
category: Character or character vector. The pathway category or categories to filter by (e.g., "GOBP", "KEGG", "GOCC"). Default is "GOBP".

Value

A data frame containing the pathway mapping information (such as gene, pathway ID, and description) for the specified categories and genes.

Examples

if (FALSE) { # \dontrun{
# Get all GO Biological Process pathways for Human (ID 96)
gobp_paths <- path_filter(species_id = 96, category = "GOBP")

# Get KEGG pathways for specific genes in a dataset
data(hypoxia_reads)
kegg_paths <- path_filter(
    species_id = 96,
    genes = rownames(hypoxia_reads)[1:100],
    category = "KEGG"
)
} # }