man/get_pathways_annotations.Rd
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 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/utils.R
 \name{get_pathways_annotations}
 \alias{get_pathways_annotations}
 \title{Get Pathways functional annotations}
 \usage{
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 get_pathways_annotations(pathway_names, metaginfo, dbannot, collapse = FALSE)
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 }
 \arguments{
 \item{pathway_names}{Character vector of the names of the pathways}
 
 \item{metaginfo}{Pathways object}
 
 \item{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.}
 
 \item{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 \code{dbannot}.
 }
 \description{
 Get functional annotation of the pathways, either for a particular
 annotation or a stored one.
 }
 \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")
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 \dontrun{get_pathways_annotations(pathway_names, pathways, "GO")}
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 get_pathways_annotations(pathway_names, pathways, "uniprot")
 
 }