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Updating DESCRIPTION and man/ files, updating .gitignore

Marta R. Hidalgo authored on 03/12/2019 15:42:36
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@@ -4,8 +4,7 @@
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 \alias{get_pathways_annotations}
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 \title{Get Pathways functional annotations}
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 \usage{
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-get_pathways_annotations(pathway_names, metaginfo, dbannot,
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-  collapse = FALSE)
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+get_pathways_annotations(pathway_names, metaginfo, dbannot, collapse = FALSE)
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 }
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 \arguments{
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 \item{pathway_names}{Character vector of the names of the pathways}
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Fixing bugs and man files

Marta R. Hidalgo authored on 21/02/2019 15:07:11
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@@ -4,7 +4,8 @@
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 \alias{get_pathways_annotations}
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 \title{Get Pathways functional annotations}
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 \usage{
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-get_pathways_annotations(pathway_names, metaginfo, dbannot, collapse = FALSE)
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+get_pathways_annotations(pathway_names, metaginfo, dbannot,
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+  collapse = FALSE)
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 }
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 \arguments{
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 \item{pathway_names}{Character vector of the names of the pathways}
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Reducing examples, v0.99.33

Marta R. Hidalgo authored on 10/04/2018 09:11:16
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@@ -32,7 +32,7 @@ pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
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 "hsa04012"))
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 pathway_names <- c("P-hsa03320-37", "P-hsa03320-61", "P-hsa03320-46",
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 "P-hsa03320-57", "P-hsa03320-64", "P-hsa03320-47", "P-hsa03320-65")
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-get_pathways_annotations(pathway_names, pathways, "GO")
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+\dontrun{get_pathways_annotations(pathway_names, pathways, "GO")}
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 get_pathways_annotations(pathway_names, pathways, "uniprot")
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 }
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Adding new MAN files

Marta R. Hidalgo authored on 14/02/2018 10:50:27
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new file mode 100644
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/utils.R
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+\name{get_pathways_annotations}
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+\alias{get_pathways_annotations}
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+\title{Get Pathways functional annotations}
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+\usage{
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+get_pathways_annotations(pathway_names, metaginfo, dbannot, collapse = FALSE)
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+}
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+\arguments{
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+\item{pathway_names}{Character vector of the names of the pathways}
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+
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+\item{metaginfo}{Pathways object}
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+
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+\item{dbannot}{Either a string indicating which precomputed annotation
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+to use ("uniprot" for Uniprot Keywords or "GO" for Gene Ontology terms),
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+or a dataframe with the annotation of the genes to the functions. First
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+column are gene symbols, second column the functions.}
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+
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+\item{collapse}{Boolean, whether to collapse all functions of the same
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+path in a single character string.}
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+}
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+\value{
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+2-columns matrix with the annotations of each pathway ID in the
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+annotation \code{dbannot}.
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+}
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+\description{
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+Get functional annotation of the pathways, either for a particular
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+annotation or a stored one.
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+}
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+\examples{
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+pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
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+"hsa04012"))
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+pathway_names <- c("P-hsa03320-37", "P-hsa03320-61", "P-hsa03320-46",
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+"P-hsa03320-57", "P-hsa03320-64", "P-hsa03320-47", "P-hsa03320-65")
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+get_pathways_annotations(pathway_names, pathways, "GO")
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+get_pathways_annotations(pathway_names, pathways, "uniprot")
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+
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+}