git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@116328 bc3139a8-67e5-0310-9ffc-ced21a209358
Calin Voichita authored on 15/04/2016 05:40:35 | ... | ... |
@@ -1,35 +1,35 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/keggDataREST.R |
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| 1 | 3 |
\name{keggPathwayGraphs}
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| 2 | 4 |
\alias{keggPathwayGraphs}
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| 3 | 5 |
\title{Download and parse KEGG pathway data}
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| 4 | 6 |
\usage{
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- keggPathwayGraphs(organism = "hsa", |
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- targRelTypes = c("GErel", "PCrel", "PPrel"),
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- relPercThresh = 0.9, nodeOnlyGraphs = FALSE, |
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- updateCache = FALSE, verbose = TRUE) |
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+keggPathwayGraphs(organism = "hsa", targRelTypes = c("GErel", "PCrel",
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+ "PPrel"), relPercThresh = 0.9, nodeOnlyGraphs = FALSE, |
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+ updateCache = FALSE, verbose = TRUE) |
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| 9 | 10 |
} |
| 10 | 11 |
\arguments{
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- \item{organism}{organism code as defined by KEGG}
|
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+\item{organism}{organism code as defined by KEGG}
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| 12 | 13 |
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- \item{targRelTypes}{target relation types}
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+\item{targRelTypes}{target relation types}
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| 14 | 15 |
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- \item{relPercThresh}{percentage of the number of relation
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- types over all possible realtions in the pathway} |
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+\item{relPercThresh}{percentage of the number of relation types over all possible realtions in the pathway}
|
|
| 17 | 17 |
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- \item{nodeOnlyGraphs}{allow graphs with no edges}
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+\item{nodeOnlyGraphs}{allow graphs with no edges}
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| 19 | 19 |
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- \item{updateCache}{re-download KEGG data}
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+\item{updateCache}{re-download KEGG data}
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| 21 | 21 |
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- \item{verbose}{show progress of downloading and parsing}
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+\item{verbose}{show progress of downloading and parsing}
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| 23 | 23 |
} |
| 24 | 24 |
\value{
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- A list of \code{\link{graphNEL}} objects encoding the
|
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- pathway information. |
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+A list of \code{\link{graphNEL}} objects encoding the pathway information.
|
|
| 27 | 26 |
} |
| 28 | 27 |
\description{
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- Download and parse KEGG pathway data |
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+Download and parse KEGG pathway data |
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| 30 | 29 |
} |
| 31 | 30 |
\examples{
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-# The pathway cache provided as part of the pathway contains only the |
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+ |
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+# The pathway cache provided as part of the pathway contains only the |
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| 33 | 33 |
# pathways that passed the default filtering. We recommend, re-downloading |
| 34 | 34 |
# the pathways using the updateCache parameter |
| 35 | 35 |
kpg <- keggPathwayGraphs("hsa")
|
| ... | ... |
@@ -43,11 +43,12 @@ head(names(kpg)) |
| 43 | 43 |
kpg[["path:hsa04110"]] |
| 44 | 44 |
head(nodes(kpg[["path:hsa04110"]])) |
| 45 | 45 |
head(edges(kpg[["path:hsa04110"]])) |
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+ |
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| 46 | 47 |
} |
| 47 | 48 |
\author{
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- Calin Voichita and Sorin Draghici |
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+Calin Voichita and Sorin Draghici |
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| 49 | 50 |
} |
| 50 | 51 |
\seealso{
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- \code{\link{keggPathwayNames}}
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+\code{\link{keggPathwayNames}}
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| 52 | 53 |
} |
| 53 | 54 |
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@75116 bc3139a8-67e5-0310-9ffc-ced21a209358
Calin Voichita authored on 31/03/2013 19:14:34 git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@74711 bc3139a8-67e5-0310-9ffc-ced21a209358
Marc Carlson authored on 22/03/2013 22:40:44 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,53 @@ |
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+\name{keggPathwayGraphs}
|
|
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+\alias{keggPathwayGraphs}
|
|
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+\title{Download and parse KEGG pathway data}
|
|
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+\usage{
|
|
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+ keggPathwayGraphs(organism = "hsa", |
|
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+ targRelTypes = c("GErel", "PCrel", "PPrel"),
|
|
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+ relPercThresh = 0.9, nodeOnlyGraphs = FALSE, |
|
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+ updateCache = FALSE, verbose = TRUE) |
|
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+} |
|
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+\arguments{
|
|
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+ \item{organism}{organism code as defined by KEGG}
|
|
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+ |
|
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+ \item{targRelTypes}{target relation types}
|
|
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+ |
|
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+ \item{relPercThresh}{percentage of the number of relation
|
|
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+ types over all possible realtions in the pathway} |
|
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+ |
|
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+ \item{nodeOnlyGraphs}{allow graphs with no edges}
|
|
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+ |
|
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+ \item{updateCache}{re-downlaod KEGG data}
|
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+ |
|
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+ \item{verbose}{show progress of downloading and parsing}
|
|
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+} |
|
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+\value{
|
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+ A list of \code{\link{graphNEL}} objects encoding the
|
|
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+ pathway information. |
|
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+} |
|
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+\description{
|
|
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+ Download and parse KEGG pathway data |
|
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+} |
|
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+\examples{
|
|
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+# The pathway cache provided as part of the pathway contains only the |
|
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+# pathways that passed the default filtering. We recommend, re-downloading |
|
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+# the pathways using the updateCache parameter |
|
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+kpg <- keggPathwayGraphs("hsa")
|
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+ |
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+# to update the pathway cache for human run: |
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+# kpg <- keggPathwayGraphs("hsa", updateCache = TRUE)
|
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+# this is time consuming and depends on the available bandwith. |
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+ |
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+head(names(kpg)) |
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+ |
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+kpg[["path:hsa04110"]] |
|
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+head(nodes(kpg[["path:hsa04110"]])) |
|
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+head(edges(kpg[["path:hsa04110"]])) |
|
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+} |
|
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+\author{
|
|
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+ Calin Voichita and Sorin Draghici |
|
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+} |
|
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+\seealso{
|
|
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+ \code{\link{keggPathwayNames}}
|
|
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+} |
|
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+ |