@@ -3,7 +3,7 @@ Title: Code for Building Annotation Database Packages

 Description: Provides code for generating Annotation packages and

 	     their databases.  Packages produced are intended to be

 	     used with AnnotationDbi.

-Version: 1.13.1

+Version: 1.13.2

 Author: Marc Carlson, Herve Pages

 Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>

 Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.15.10),

@@ -15,19 +15,31 @@

   \url{http://www.genome.ad.jp/kegg/}

 }

-\examples{

-  x <- @ANNOBJPREFIX@ARACYC

-  # Get the tair identifiers that are mapped to pathways

-  mapped_tairs <- mappedkeys(x)

-  # Convert to a list

-  xx <- as.list(x[mapped_tairs])

-  if(length(xx) > 0) {

-    # Get the pathways for the first five tairs

-    xx[1:5]

-    # For the first tair

-    xx[[1]]

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

   }

 }

+\examples{

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+x <- @ANNOBJPREFIX@ARACYC

+# Get the tair identifiers that are mapped to pathways

+mapped_tairs <- mappedkeys(x)

+# Convert to a list

+xx <- as.list(x[mapped_tairs])

+if(length(xx) > 0) {

+  # Get the pathways for the first five tairs

+  xx[1:5]

+  # For the first tair

+  xx[[1]]

+}

+}

+

 \keyword{datasets}

@@ -5,6 +5,7 @@

   @ANNOBJPREFIX@ARACYCENZYME is an R object that provides mappings between

   TAIR identifiers and Enzyme Names from ARACYC. 

 }

+

 \details{

   Each TAIR identifier maps to a named vector containing the

   Enzyme name for that gene according to the ARACYC database.  If this

@@ -13,18 +14,31 @@

   Mappings between tair identifiers and enzyme identifiers were obtained using files

   provided by: @ENZYMESOURCE@

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-        x <- @ANNOBJPREFIX@ARACYCENZYME

-        # Get the tair identifiers that are mapped to an Enzyme Name 

-        mapped_tairs <- mappedkeys(x)

-        # Convert to a list

-        xx <- as.list(x[mapped_tairs])

-        if(length(xx) > 0) {

-          # Get the ENZYME name for the first five tairs

-          xx[1:5]

-          # Get the first one

-          xx[[1]]

-        }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+x <- @ANNOBJPREFIX@ARACYCENZYME

+# Get the tair identifiers that are mapped to an Enzyme Name 

+mapped_tairs <- mappedkeys(x)

+# Convert to a list

+xx <- as.list(x[mapped_tairs])

+if(length(xx) > 0) {

+  # Get the ENZYME name for the first five tairs

+  xx[1:5]

+  # Get the first one

+  xx[[1]]

+}

 }

 \keyword{datasets}

@@ -8,14 +8,27 @@

   this package is to provide detailed information about the

   @ANNOBJPREFIX@ platform. This package is updated biannually.

-  You can learn what objects this package supports with the following command:

+  Objects in this package are accessed using the \code{select()} interface.

+  See ?select in the AnnotationDbi package for details.

+}

-  \code{ls("package:@ANNOBJPREFIX@.db")} 

-  

-  Each of these objects has their own manual page detailing where

-  relevant data was obtained along with some examples of how to use it.

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          \code{keys()}, \code{columns()} and \code{select()}.

+  }

 }

+

 \examples{

-  ls("package:@ANNOBJPREFIX@.db")

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+columns(@ANNOBJPREFIX@.db)

+

+## Bimap interface:

+## The 'old style' of interacting with these objects is manipulation as 

+## bimaps. While this approach is still available we strongly encourage the

+## use of select().

+ls("package:@ANNOBJPREFIX@.db")

 }

 \keyword{datasets}

@@ -16,18 +16,30 @@

 }

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-        x <- @ANNOBJPREFIX@CHR

-        # Get the tair identifiers that are mapped to a chromosome

-        mapped_tairs <- mappedkeys(x)

-        # Convert to a list

-        xx <- as.list(x[mapped_tairs])

-        if(length(xx) > 0) {

-          # Get the CHR for the first five tairs

-          xx[1:5]

-          # Get the first one

-          xx[[1]]

-        }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+x <- @ANNOBJPREFIX@CHR

+# Get the tair identifiers that are mapped to a chromosome

+mapped_tairs <- mappedkeys(x)

+# Convert to a list

+xx <- as.list(x[mapped_tairs])

+if(length(xx) > 0) {

+  # Get the CHR for the first five tairs

+  xx[1:5]

+  # Get the first one

+  xx[[1]]

+}

 }

 \keyword{datasets}

@@ -5,6 +5,7 @@

   @ANNOBJPREFIX@CHRLENGTHS provides the length measured in base pairs for

   each of the chromosomes. 

 }

+

 \details{

    This is a named vector with chromosome numbers as the names and the

    corresponding lengths for chromosomes as the values.

@@ -13,10 +14,23 @@

    number of base pairs on the sequence string for each chromosome.

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-    tt <- @ANNOBJPREFIX@CHRLENGTHS

-    # Length of chromosome 1

-    tt["1"]

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+tt <- @ANNOBJPREFIX@CHRLENGTHS

+# Length of chromosome 1

+tt["1"]

 }

 \keyword{datasets}

@@ -25,18 +25,31 @@

   Mappings were based on data provided by: @CHRLOCSOURCE@

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-        x <- @ANNOBJPREFIX@CHRLOC

-        # Get the tair identifiers that are mapped to chromosome locations

-        mapped_tairs <- mappedkeys(x)

-        # Convert to a list

-        xx <- as.list(x[mapped_tairs])

-        if(length(xx) > 0) {

-          # Get the CHRLOC for the first five tairs

-          xx[1:5]

-          # Get the first one

-          xx[[1]]

-        }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+x <- @ANNOBJPREFIX@CHRLOC

+# Get the tair identifiers that are mapped to chromosome locations

+mapped_tairs <- mappedkeys(x)

+# Convert to a list

+xx <- as.list(x[mapped_tairs])

+if(length(xx) > 0) {

+  # Get the CHRLOC for the first five tairs

+  xx[1:5]

+  # Get the first one

+  xx[[1]]

+}

 }

 \keyword{datasets}

@@ -14,18 +14,30 @@

   \url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA}

 }

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-    x <- @ANNOBJPREFIX@ENTREZID

-    # Get the ORF IDs that are mapped to an Entrez Gene ID

-    mapped_genes <- mappedkeys(x)

-    # Convert to a list

-    xx <- as.list(x[mapped_genes])

-    if(length(xx) > 0) {

-      # Get the Entrez gene IDs for the first five genes

-      xx[1:5]

-      # Get the first one

-      xx[[1]]

-    }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+x <- @ANNOBJPREFIX@ENTREZID

+# Get the ORF IDs that are mapped to an Entrez Gene ID

+mapped_genes <- mappedkeys(x)

+# Convert to a list

+xx <- as.list(x[mapped_genes])

+if(length(xx) > 0) {

+  # Get the Entrez gene IDs for the first five genes

+  xx[1:5]

+  # Get the first one

+  xx[[1]]

+}

 }

 \keyword{datasets}

@@ -47,18 +47,31 @@

 \references{

 \url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-        x <- @ANNOBJPREFIX@ENZYME

-        # Get the TAIR identifiers that are mapped to an EC number 

-        mapped_tairs <- mappedkeys(x)

-        # Convert to a list

-        xx <- as.list(x[mapped_tairs])

-        if(length(xx) > 0) {

-          # Get the ENZYME for the first five tairs

-          xx[1:5]

-          # Get the first one

-          xx[[1]]

-        }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+x <- @ANNOBJPREFIX@ENZYME

+# Get the TAIR identifiers that are mapped to an EC number 

+mapped_tairs <- mappedkeys(x)

+# Convert to a list

+xx <- as.list(x[mapped_tairs])

+if(length(xx) > 0) {

+  # Get the ENZYME for the first five tairs

+  xx[1:5]

+  # Get the first one

+  xx[[1]]

+}

 }

 \keyword{datasets}

@@ -46,15 +46,20 @@

 \url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}

 }

 \examples{

-    # Convert to a list

-    xx <- as.list(@ANNOBJPREFIX@ENZYME2TAIR)

-   if(length(xx) > 0){

-       # Gets the tair identifiers for the first five enzyme

-       #commission numbers

-       xx[1:5]

-       # Get the first one

-       xx[[1]]

-    }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+# Convert to a list

+xx <- as.list(@ANNOBJPREFIX@ENZYME2TAIR)

+if(length(xx) > 0){

+    # Gets the tair identifiers for the first five enzyme

+    #commission numbers

+    xx[1:5]

+    # Get the first one

+    xx[[1]]

+}

 }

 \keyword{datasets}

@@ -5,6 +5,7 @@

   @ANNOBJPREFIX@GENENAME is an R object that maps TAIR

   identifiers to the corresponding gene name.

 }

+

 \details{

   Each TAIR identifier maps to a named vector containing the gene

   name. The vector name corresponds to the TAIR identifier. If

@@ -19,18 +20,30 @@

 }

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-        x <- @ANNOBJPREFIX@GENENAME

-        # Get the TAIR identifiers that are mapped to a gene name

-        mapped_tairs <- mappedkeys(x)

-        # Convert to a list

-        xx <- as.list(x[mapped_tairs])

-        if(length(xx) > 0) {

-          # Get the GENENAME for the first five tairs

-          xx[1:5]

-          # Get the first one

-          xx[[1]]

-        }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+x <- @ANNOBJPREFIX@GENENAME

+# Get the TAIR identifiers that are mapped to a gene name

+mapped_tairs <- mappedkeys(x)

+# Convert to a list

+xx <- as.list(x[mapped_tairs])

+if(length(xx) > 0) {

+  # Get the GENENAME for the first five tairs

+  xx[1:5]

+  # Get the first one

+  xx[[1]]

+}

 }

 \keyword{datasets}

@@ -69,35 +69,47 @@

   Ontology terms and other information are available in a separate data

   package named GO.

 }

-\seealso{

-  \code{\link{@ANNOBJPREFIX@GO2ALLTAIRS}}.

-}

+

 \references{

 \url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/}

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link{@ANNOBJPREFIX@GO2ALLTAIRS}}.

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-    x <- @ANNOBJPREFIX@GO

-    # Get the TAIR gene identifiers that are mapped to a GO ID

-    mapped_genes <- mappedkeys(x)

-    # Convert to a list

-    xx <- as.list(x[mapped_genes])

-    if(length(xx) > 0) {

-        # Try the first one

-        got <- xx[[1]]           

-        got[[1]][["GOID"]]

-        got[[1]][["Ontology"]]

-        got[[1]][["Evidence"]]

-    }

-    # For the reverse map:

-    # Convert to a list

-    xx <- as.list(@ANNOBJPREFIX@GO2TAIR)

-    if(length(xx) > 0){

-        # Gets the TAIR gene ids for the top 2nd and 3nd GO identifiers

-        goids <- xx[2:3]

-        # Gets the TAIR ids for the first element of goids

-        goids[[1]]

-        # Evidence code for the mappings

-        names(goids[[1]])

-    }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+x <- @ANNOBJPREFIX@GO

+# Get the TAIR gene identifiers that are mapped to a GO ID

+mapped_genes <- mappedkeys(x)

+# Convert to a list

+xx <- as.list(x[mapped_genes])

+if(length(xx) > 0) {

+    # Try the first one

+    got <- xx[[1]]           

+    got[[1]][["GOID"]]

+    got[[1]][["Ontology"]]

+    got[[1]][["Evidence"]]

+}

+# For the reverse map:

+# Convert to a list

+xx <- as.list(@ANNOBJPREFIX@GO2TAIR)

+if(length(xx) > 0){

+    # Gets the TAIR gene ids for the top 2nd and 3nd GO identifiers

+    goids <- xx[2:3]

+    # Gets the TAIR ids for the first element of goids

+    goids[[1]]

+    # Evidence code for the mappings

+    names(goids[[1]])

+}

 }

 \keyword{datasets}

@@ -61,20 +61,34 @@

   relationships indicate that the genes from the child terms would be

   the same kind of thing.

 }

+

 \references{

 \url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/}

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-    # Convert to a list

-    xx <- as.list(@ANNOBJPREFIX@GO2ALLTAIRS)

-    if(length(xx) > 0){

-        # Gets the tair identifiers for the top 2nd and 3nd GO identifiers

-        goids <- xx[2:3]

-        # Gets all the tair identifiers for the first element of goids

-        goids[[1]]

-        # Evidence code for the mappings

-        names(goids[[1]])

-    }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+# Convert to a list

+xx <- as.list(@ANNOBJPREFIX@GO2ALLTAIRS)

+if(length(xx) > 0){

+    # Gets the tair identifiers for the top 2nd and 3nd GO identifiers

+    goids <- xx[2:3]

+    # Gets all the tair identifiers for the first element of goids

+    goids[[1]]

+    # Evidence code for the mappings

+    names(goids[[1]])

+}

 }

 \keyword{datasets}

@@ -21,21 +21,30 @@

 }

 \seealso{

-  \code{\link[AnnotationDbi:Bimap-keys]{mappedkeys}},

-  \code{\link[AnnotationDbi:Bimap-keys]{count.mappedkeys}},

-  \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}}

+  \itemize{

+    \item \code{\link[AnnotationDbi:Bimap-keys]{mappedkeys}}

+    \item \code{\link[AnnotationDbi:Bimap-keys]{count.mappedkeys}}

+    \item \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}}

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

 }

 \examples{

-  @ANNOBJPREFIX@MAPCOUNTS

-  mapnames <- names(@ANNOBJPREFIX@MAPCOUNTS)

-  @ANNOBJPREFIX@MAPCOUNTS[mapnames[1]]

-  x <- get(mapnames[1])

-  sum(!is.na(as.list(x)))

-  count.mappedkeys(x)   # much faster!

-

-  ## Check the "map count" of all the maps in package @PKGNAME@

-  checkMAPCOUNTS("@PKGNAME@")

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+@ANNOBJPREFIX@MAPCOUNTS

+mapnames <- names(@ANNOBJPREFIX@MAPCOUNTS)

+@ANNOBJPREFIX@MAPCOUNTS[mapnames[1]]

+x <- get(mapnames[1])

+sum(!is.na(as.list(x)))

+count.mappedkeys(x)   # much faster!

+

+## Check the "map count" of all the maps in package @PKGNAME@

+checkMAPCOUNTS("@PKGNAME@")

 }

 \keyword{datasets}

@@ -5,13 +5,27 @@

   @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a

   character string that names the organism for which @ANNOBJPREFIX@ was built.

 }

+

 \details{

   Although the package name is suggestive of the organism for which it

   was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically

   extract the organism name.

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-  @ANNOBJPREFIX@ORGANISM

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+@ANNOBJPREFIX@ORGANISM

 }

 \keyword{datasets}

@@ -23,18 +23,31 @@

 \references{

   \url{http://www.genome.ad.jp/kegg/}

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-        x <- @ANNOBJPREFIX@PATH

-        # Get the TAIR identifiers that are mapped to a KEGG pathway ID

-        mapped_genes <- mappedkeys(x)

-        # Convert to a list

-        xx <- as.list(x[mapped_genes])

-        if(length(xx) > 0) {

-          # Get the PATH for the first five genes

-          xx[1:5]

-          # Get the first one

-          xx[[1]]

-        }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+x <- @ANNOBJPREFIX@PATH

+# Get the TAIR identifiers that are mapped to a KEGG pathway ID

+mapped_genes <- mappedkeys(x)

+# Convert to a list

+xx <- as.list(x[mapped_genes])

+if(length(xx) > 0) {

+  # Get the PATH for the first five genes

+  xx[1:5]

+  # Get the first one

+  xx[[1]]

+}

 }

 \keyword{datasets}

@@ -24,20 +24,34 @@

   Mappings were based on data provided by: @PATH2TAIRSOURCE@

 }

+

 \references{

 \url{http://www.genome.ad.jp/kegg/}

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-    # Convert the object to a list

-    xx <- as.list(@ANNOBJPREFIX@PATH2TAIR)

-    # Remove pathway identifiers that do not map to any tair id

-    xx <- xx[!is.na(xx)]

-    if(length(xx) > 0){

-        # The tair identifiers for the first two elements of XX

-        xx[1:2]

-        # Get the first one

-        xx[[1]]

-    } 

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+# Convert the object to a list

+xx <- as.list(@ANNOBJPREFIX@PATH2TAIR)

+# Remove pathway identifiers that do not map to any tair id

+xx <- xx[!is.na(xx)]

+if(length(xx) > 0){

+    # The tair identifiers for the first two elements of XX

+    xx[1:2]

+    # Get the first one

+    xx[[1]]

+} 

 }

 \keyword{datasets}

@@ -20,28 +20,42 @@

   Mappings were based on data provided by: @PMIDSOURCE@

 }

+

 \references{

   \url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed}

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-        x <- @ANNOBJPREFIX@PMID

-        # Get the tair identifiers that are mapped to any PubMed ID

-        mapped_genes <- mappedkeys(x)

-        # Convert to a list

-        xx <- as.list(x[mapped_genes])

-    if(length(xx) > 0){

-        # The tair identifiers for the first two elements of XX

-        xx[1:2]

-        # Get the first one

-        xx[[1]]

-        if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]])

-           && require(annotate)){

-            # Gets article information as XML files

-            xmls <- pubmed(xx[[1]], disp = "data")

-            # Views article information using a browser

-            pubmed(xx[[1]], disp = "browser")

-        }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+x <- @ANNOBJPREFIX@PMID

+# Get the tair identifiers that are mapped to any PubMed ID

+mapped_genes <- mappedkeys(x)

+# Convert to a list

+xx <- as.list(x[mapped_genes])

+if(length(xx) > 0){

+    # The tair identifiers for the first two elements of XX

+    xx[1:2]

+    # Get the first one

+    xx[[1]]

+    if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]])

+        && require(annotate)){

+        # Gets article information as XML files

+        xmls <- pubmed(xx[[1]], disp = "data")

+        # Views article information using a browser

+        pubmed(xx[[1]], disp = "browser")

     }

 }

+}

 \keyword{datasets}

@@ -20,22 +20,34 @@

 }

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-    # Convert the object to a list

-    xx <- as.list(@ANNOBJPREFIX@PMID2TAIR)

-    if(length(xx) > 0){

-        # The tair identifiers for the first two elements of XX

-        xx[1:2]

-        # Get the first one

-        xx[[1]]

-        if(interactive() && require(annotate)){

-            # Gets article information as XML files for a PubMed id

-            xmls <- pubmed(names(xx)[1], disp = "data")

-            # Views article information using a browser

-            pubmed(names(xx)[1], disp = "browser")

-        }

+## select() interface:

+## Objects in this package can be accessed using the select() interface

+## from the AnnotationDbi package. See ?select for details.

+

+## Bimap interface:

+# Convert the object to a list

+xx <- as.list(@ANNOBJPREFIX@PMID2TAIR)

+if(length(xx) > 0){

+    # The tair identifiers for the first two elements of XX

+    xx[1:2]

+    # Get the first one

+    xx[[1]]

+    if(interactive() && require(annotate)){

+        # Gets article information as XML files for a PubMed id

+        xmls <- pubmed(names(xx)[1], disp = "data")

+        # Views article information using a browser

+        pubmed(names(xx)[1], disp = "browser")

     }

 }

+}

 \keyword{datasets}

@@ -42,35 +42,49 @@

   \url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA}

 }

+

 \references{

     \url{http://www.ncbi.nlm.nih.gov}

     \url{http://www.ncbi.nlm.nih.gov/RefSeq/} 

 }

+

+\seealso{

+  \itemize{

+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of

+          the \code{select()} interface.

+  }

+}

+

 \examples{

-        x <- @ANNOBJPREFIX@REFSEQ

-        # Get the TAIR identifiers that are mapped to any RefSeq ID

-        mapped_genes <- mappedkeys(x)

-        # Convert to a list

-        xx <- as.list(x[mapped_genes])

-        if(length(xx) > 0) {

-          # Get the REFSEQ for the first five genes

-          xx[1:5]

-          # Get the first one

-          xx[[1]]

-        }

-

-        # For the reverse map:

-        x <- @ANNOBJPREFIX@REFSEQ2TAIR

-        # Get the RefSeq identifier that are mapped to an TAIR ID

-        mapped_seqs <- mappedkeys(x)

-        # Convert to a list