Browse code

added novel method and increase version to 1.99

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
Showing1 changed files
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@@ -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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 \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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+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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 }
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 \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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-  \item{targRelTypes}{target relation types}
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+\item{targRelTypes}{target relation types}
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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}
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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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-  \item{updateCache}{re-download KEGG data}
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+\item{updateCache}{re-download KEGG data}
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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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 }
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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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+A list of \code{\link{graphNEL}} objects encoding the 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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+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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+
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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")
... ...
@@ -43,11 +43,12 @@ head(names(kpg))
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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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 }
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 \author{
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-  Calin Voichita and Sorin Draghici
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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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+\code{\link{keggPathwayNames}}
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 }
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Browse code

added plot functionalities; updated documentation; removed 3.0.0 dependency; fixed bugs

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
Showing1 changed files
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@@ -17,7 +17,7 @@
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   \item{nodeOnlyGraphs}{allow graphs with no edges}
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-  \item{updateCache}{re-downlaod KEGG data}
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+  \item{updateCache}{re-download KEGG data}
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   \item{verbose}{show progress of downloading and parsing}
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 }
Browse code

Add BaseSpaceR CNORfeeder eiR and ROntoTools to the repos.

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
Showing1 changed files
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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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+