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 | ... | ... |
@@ -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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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 | 1 | 1 |
new file mode 100644 |
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@@ -0,0 +1,40 @@ |
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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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+ |