get_pathways_annotations {hipathia} | R Documentation

## 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")

[Package hipathia version 2.0.0 Index]