Marta R. Hidalgo authored on 03/12/2019 15:42:36 | ... | ... |
@@ -4,8 +4,7 @@ |
| 4 | 4 |
\alias{get_pathways_annotations}
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| 5 | 5 |
\title{Get Pathways functional annotations}
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| 6 | 6 |
\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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Marta R. Hidalgo authored on 21/02/2019 15:07:11 | ... | ... |
@@ -4,7 +4,8 @@ |
| 4 | 4 |
\alias{get_pathways_annotations}
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| 5 | 5 |
\title{Get Pathways functional annotations}
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| 6 | 6 |
\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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| 8 | 9 |
} |
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\arguments{
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| 10 | 11 |
\item{pathway_names}{Character vector of the names of the pathways}
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Marta R. Hidalgo authored on 10/04/2018 09:11:16 | ... | ... |
@@ -32,7 +32,7 @@ pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
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| 32 | 32 |
"hsa04012")) |
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pathway_names <- c("P-hsa03320-37", "P-hsa03320-61", "P-hsa03320-46",
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| 34 | 34 |
"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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| 36 | 36 |
get_pathways_annotations(pathway_names, pathways, "uniprot") |
| 37 | 37 |
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| 38 | 38 |
} |
Marta R. Hidalgo authored on 14/02/2018 10:50:27 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,38 @@ |
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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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+} |