Browse code

update AnnDbPkg template man to reference select() interface

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@109954 bc3139a8-67e5-0310-9ffc-ced21a209358

Valerie Obenchain authored on 27/10/2015 02:29:44
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@@ -23,18 +23,31 @@
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 \references{
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   \url{http://www.genome.ad.jp/kegg/}
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 }
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+
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+\seealso{
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+  \itemize{
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+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
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+          the \code{select()} interface.
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+  }
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+}
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+
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 \examples{
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-        x <- @ANNOBJPREFIX@PATH
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-        # Get the probe identifiers that are mapped to a KEGG pathway ID
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-        mapped_probes <- mappedkeys(x)
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-        # Convert to a list
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-        xx <- as.list(x[mapped_probes])
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-        if(length(xx) > 0) {
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-          # Get the PATH for the first five probes
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-          xx[1:5]
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-          # Get the first one
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-          xx[[1]]
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-        }
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+## select() interface:
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+## Objects in this package can be accessed using the select() interface
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+## from the AnnotationDbi package. See ?select for details.
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+
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+## Bimap interface:
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+x <- @ANNOBJPREFIX@PATH
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+# Get the probe identifiers that are mapped to a KEGG pathway ID
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+mapped_probes <- mappedkeys(x)
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+# Convert to a list
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+xx <- as.list(x[mapped_probes])
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+if(length(xx) > 0) {
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+  # Get the PATH for the first five probes
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+  xx[1:5]
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+  # Get the first one
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+  xx[[1]]
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+}
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 }
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 \keyword{datasets}
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Browse code

Splits AnnoationDbi into AnnotationDbi and AnnotationForge

All the resources for creating annotations are getting bulky and need
to be put into another place. We are calling that place
AnnotationForge.


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@66999 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 25/06/2012 18:39:17
Showing1 changed files
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new file mode 100644
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+\name{@ANNOBJPREFIX@PATH}
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+\alias{@ANNOBJPREFIX@PATH}
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+\title{Mappings between probe identifiers and KEGG pathway identifiers}
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+\description{
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+  KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data
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+  for various organisms. @ANNOBJPREFIX@PATH maps probe identifiers to the
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+  identifiers used by KEGG for pathways in which the genes represented
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+  by the probe identifiers are involved
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+}
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+\details{
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+  Each KEGG pathway has a name and identifier. Pathway name for a given pathway
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+  identifier can be obtained using the KEGG data package that can either be
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+  built using AnnBuilder or downloaded from Bioconductor
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+  \url{http://www.bioconductor.org}.
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+
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+  Graphic presentations of pathways are searchable at
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+  url http://www.genome.ad.jp/kegg/pathway.html by using pathway identifiers as
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+  keys.   
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+
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+  Mappings were based on data provided by: @PATHSOURCE@
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+
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+}
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+\references{
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+  \url{http://www.genome.ad.jp/kegg/}
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+}
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+\examples{
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+        x <- @ANNOBJPREFIX@PATH
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+        # Get the probe identifiers that are mapped to a KEGG pathway ID
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+        mapped_probes <- mappedkeys(x)
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+        # Convert to a list
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+        xx <- as.list(x[mapped_probes])
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+        if(length(xx) > 0) {
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+          # Get the PATH for the first five probes
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+          xx[1:5]
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+          # Get the first one
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+          xx[[1]]
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+        }
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+}
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+\keyword{datasets}
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+