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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
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+\name{@ANNOBJPREFIX@PATH}
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+\alias{@ANNOBJPREFIX@PATH}
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+\alias{@ANNOBJPREFIX@PATH2ORF}
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+\title{Mappings between ORF 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 ORF identifiers to the
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+  identifiers used by KEGG for pathways
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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 ORF identifiers that are mapped to a KEGG pathway ID
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+    mapped_genes <- mappedkeys(x)
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+    # Convert to a list
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+    xx <- as.list(x[mapped_genes])
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+    if(length(xx) > 0) {
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+      # Get the PATH for the first five genes
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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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+    # For the reverse map:
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+    # Convert the object to a list
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+    xx <- as.list(@ANNOBJPREFIX@PATH2ORF)
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+    # Remove pathway identifiers that do not map to any ORF id
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+    xx <- xx[!is.na(xx)]
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+    if(length(xx) > 0){
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+        # The ORF identifiers for the first two elements of XX
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+        xx[1:2]
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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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+