get_pathways_annotations: Get Pathways functional annotations

In martahidalgo/hipathia: HiPathia: High-throughput Pathway Analysis

Get Pathways functional annotations

Description

Get functional annotation of the pathways, either for a particular annotation or a stored one.

Usage

get_pathways_annotations(pathway_names, metaginfo, dbannot, collapse = FALSE)

Arguments

pathway_names	Character vector of the names of the pathways
metaginfo	Pathways object
dbannot	Either a string indicating which precomputed annotation to use ("uniprot" for Uniprot Keywords or "GO" for Gene Ontology terms), or a dataframe with the annotation of the genes to the functions. First column are gene symbols, second column the functions.
collapse	Boolean, whether to collapse all functions of the same path in a single character string.

Value

2-columns matrix with the annotations of each pathway ID in the annotation dbannot.

Examples

pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
"hsa04012"))
pathway_names <- c("P-hsa03320-37", "P-hsa03320-61", "P-hsa03320-46",
"P-hsa03320-57", "P-hsa03320-64", "P-hsa03320-47", "P-hsa03320-65")
## Not run: get_pathways_annotations(pathway_names, pathways, "GO")
get_pathways_annotations(pathway_names, pathways, "uniprot")

martahidalgo/hipathia documentation built on Jan. 12, 2023, 1:44 p.m.