1. AnnotationForge
  2. Commit a92ed3ec85bef04d7a8ae42e84dee716cc03070f
Browse code

last round of updates to template man pages to reference select()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge@110078 bc3139a8-67e5-0310-9ffc-ced21a209358

Valerie Obenchain authored on 29/10/2015 20:46:44
Showing 138 changed files
DESCRIPTION
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@@ -3,7 +3,7 @@ Title: Code for Building Annotation Database Packages
3 3 
 Description: Provides code for generating Annotation packages and
4 4 
 	     their databases.  Packages produced are intended to be
5 5 
 	     used with AnnotationDbi.
6 
-Version: 1.13.3
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+Version: 1.13.4
7 7 
 Author: Marc Carlson, Herve Pages
8 8 
 Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
9 9 
 Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.15.10),
inst/AnnDbPkg-templates/COELICOLOR.DB/man/ACCNUM.Rd
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@@ -8,8 +8,8 @@
8 8 
 }
9 9 
 \details{
10 10 
   This object is a simple mapping of Entrez Gene identifiers
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-  \url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to all possible GenBank
12 
-  accession numbers.
11 
+  \url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to all possible
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+  GenBank accession numbers.
13 13
14 14 
   Mappings were based on data provided by: @ACCNUMSOURCE@
15 15 
 }
inst/AnnDbPkg-templates/COELICOLOR.DB/man/BASE.Rd
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@@ -7,9 +7,8 @@
7 7 
   Welcome to the @ANNOBJPREFIX@.db annotation Package.  This is an
8 8 
   organism specific package.  The purpose is to provide detailed
9 9 
   information about the species abbreviated in the second part of the
10 
-  package name @ANNOBJPREFIX@.db.  "Hs" is for Homo sapiens.  This
11 
-  package is updated biannually.
12 
-
10 
+  package name @ANNOBJPREFIX@.db. This package is updated biannually.
11 
+
13 12 
   Objects in this package are accessed using the \code{select()} interface.
14 13 
   See ?select in the AnnotationDbi package for details.
15 14 
 }
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@@ -33,5 +32,5 @@ columns(@ANNOBJPREFIX@.db)
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 ## use of select().
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 ls("package:@ANNOBJPREFIX@.db")
35 34 
 }
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-\keyword{datasets}
37 35
36 
+\keyword{datasets}
inst/AnnDbPkg-templates/MALARIA.DB/man/BASE.Rd
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... ... 
@@ -5,10 +5,9 @@
5 5 
 \description{
6 6
7 7 
   Welcome to the @ANNOBJPREFIX@.db annotation Package.  This is an
8 
-  organism specific package.  The purpose is to provide detailed
8 
+  organism specific package. The purpose is to provide detailed
9 9 
   information about the species abbreviated in the second part of the
10 
-  package name @ANNOBJPREFIX@.db.  "Hs" is for Homo sapiens.  This
11 
-  package is updated biannually.
10 
+  package name @ANNOBJPREFIX@.db. This package is updated biannually.
12 11
13 12 
   Objects in this package are accessed using the \code{select()} interface.
14 13 
   See ?select in the AnnotationDbi package for details.
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ACCNUM.Rd
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@@ -6,27 +6,40 @@
6 6 
   manufacturer's identifiers and manufacturers accessions.
7 7 
 }
8 8 
 \details{
9 
-  For chip packages such as this, the ACCNUM mapping comes directly from
10 
-  the manufacturer.  This is different from other mappings which are
11 
-  mapped onto the probes via an Entrez Gene identifier.
9 
+  For chip packages such as this, the ACCNUM mapping comes directly from the
10 
+  manufacturer.  This is different from other mappings which are mapped onto
11 
+  the probes via an Entrez Gene identifier.
12 12
13 
-  Each manufacturer identifier maps to a vector containing a GenBank accession number.
13 
+  Each manufacturer identifier maps to a vector containing a GenBank accession
14 
+  number.
14 15
15 16 
   Mappings were based on data provided by: @ACCNUMSOURCE@
16 17 
 }
17 18
19 
+\seealso{
20 
+  \itemize{
21 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
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+          the \code{select()} interface.
23 
+  }
24 
+}
25 
+
18 26 
 \examples{
19 
-        x <- @ANNOBJPREFIX@ACCNUM
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-        # Get the probe identifiers that are mapped to an ACCNUM
21 
-        mapped_probes <- mappedkeys(x)
22 
-        # Convert to a list
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-        xx <- as.list(x[mapped_probes])
24 
-        if(length(xx) > 0) {
25 
-          # Get the ACCNUM 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]]
29 
-        }
27 
+## 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.
30 
+
31 
+## Bimap interface:
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+x <- @ANNOBJPREFIX@ACCNUM
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+# Get the probe identifiers that are mapped to an ACCNUM
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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 ACCNUM 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]]
42 
+}
30 43 
 }
31 44 
 \keyword{datasets}
32 45
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ALIAS2PROBE.Rd
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@@ -6,27 +6,39 @@
6 6 
   common gene symbol identifiers and manufacturer identifiers.
7 7 
 }
8 8 
 \details{
9 
-  Each gene symbol is mapped to a named vector of manufacturer identifiers. The name
10 
-  represents the gene symbol and the vector contains all manufacturer identifiers
11 
-  that are found for that symbol. An \code{NA} is reported for any gene symbol that
12 
-  cannot be mapped to any manufacturer identifiers.
9 
+  Each gene symbol is mapped to a named vector of manufacturer identifiers. The
10 
+  name represents the gene symbol and the vector contains all manufacturer
11 
+  identifiers that are found for that symbol. An \code{NA} is reported for any
12 
+  gene symbol that cannot be mapped to any manufacturer identifiers.
13 13
14 
-  This mapping includes ALL gene symbols including those which are already listed
15 
-  in the SYMBOL map.  The SYMBOL map is meant to only list official gene symbols,
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-  while the ALIAS maps are meant to store all used symbols.
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+  This mapping includes ALL gene symbols including those which are already
15 
+  listed in the SYMBOL map.  The SYMBOL map is meant to only list official gene
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+  symbols, while the ALIAS maps are meant to store all used symbols.
17 17
18 18 
   Mappings were based on data provided by: @ALIAS2PROBESOURCE@
19 19 
 }
20 
+
21 
+\seealso{
22 
+  \itemize{
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+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
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+          the \code{select()} interface.
25 
+  }
26 
+}
27 
+
20 28 
 \examples{
21 
-    # Convert the object to a list
22 
-    xx <- as.list(@ANNOBJPREFIX@ALIAS2PROBE)
23 
-    if(length(xx) > 0){
24 
-        # Get the probe identifiers for the first two aliases
25 
-        xx[1:2]
26 
-        # Get the first one
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-        xx[[1]]
28 
-    }
29 
+## select() interface:
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+## Objects in this package can be accessed using the select() interface
31 
+## from the AnnotationDbi package. See ?select for details.
29 32
33 
+## Bimap interface:
34 
+# Convert the object to a list
35 
+xx <- as.list(@ANNOBJPREFIX@ALIAS2PROBE)
36 
+if(length(xx) > 0){
37 
+    # Get the probe identifiers for the first two aliases
38 
+    xx[1:2]
39 
+    # Get the first one
40 
+    xx[[1]]
41 
+}
30 42 
 }
31 43
32 44 
 \keyword{datasets}
inst/AnnDbPkg-templates/NCBICHIP.DB/man/BASE.Rd
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@@ -7,16 +7,30 @@
7 7 
   Welcome to the @ANNOBJPREFIX@.db annotation Package.  The purpose of
8 8 
   this package is to provide detailed information about the
9 9 
   @ANNOBJPREFIX@ platform. This package is updated biannually.
10 
-
11 
-  You can learn what objects this package supports with the following command:
12 10
13 
-  \code{ls("package:@ANNOBJPREFIX@.db")}
14 
-
15 
-  Each of these objects has their own manual page detailing where
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-  relevant data was obtained along with some examples of how to use it.
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+  Objects in this package are accessed using the \code{select()} interface.
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+  See ?select in the AnnotationDbi package for details.
13 
+}
14 
+
15 
+\seealso{
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+  \itemize{
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+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
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+          \code{keys()}, \code{columns()} and \code{select()}.
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+  }
17 20 
 }
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+
18 22 
 \examples{
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-  ls("package:@ANNOBJPREFIX@.db")
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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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+columns(@ANNOBJPREFIX@.db)
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+
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+## Bimap interface:
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+## The 'old style' of interacting with these objects is manipulation as
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+## bimaps. While this approach is still available we strongly encourage the
31 
+## use of select().
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+ls("package:@ANNOBJPREFIX@.db")
20 33 
 }
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+
21 35 
 \keyword{datasets}
22 36
inst/AnnDbPkg-templates/NCBICHIP.DB/man/CHR.Rd
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@@ -5,6 +5,7 @@
5 5 
  @ANNOBJPREFIX@CHR is an R object that provides mappings between a
6 6 
  manufacturer identifier and the chromosome that contains the gene of interest.
7 7 
 }
8 
+
8 9 
 \details{
9 10 
   Each manufacturer identifier maps to a vector of chromosomes. Due to
10 11 
   inconsistencies that may exist at the time the object was built,
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@@ -13,21 +14,32 @@
13 14 
   the vector will contain an \code{NA}.
14 15
15 16 
   Mappings were based on data provided by: @CHRSOURCE@
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-
17 
+}
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+
19 
+\seealso{
20 
+  \itemize{
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+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
22 
+          the \code{select()} interface.
23 
+  }
17 24 
 }
18 25
19 26 
 \examples{
20 
-        x <- @ANNOBJPREFIX@CHR
21 
-        # Get the probe identifiers that are mapped to a chromosome
22 
-        mapped_probes <- mappedkeys(x)
23 
-        # Convert to a list
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-        xx <- as.list(x[mapped_probes])
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-        if(length(xx) > 0) {
26 
-          # Get the CHR for the first five probes
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-          xx[1:5]
28 
-          # Get the first one
29 
-          xx[[1]]
30 
-        }
27 
+## select() interface:
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+## Objects in this package can be accessed using the select() interface
29 
+## from the AnnotationDbi package. See ?select for details.
30 
+
31 
+## Bimap interface:
32 
+x <- @ANNOBJPREFIX@CHR
33 
+# Get the probe identifiers that are mapped to a chromosome
34 
+mapped_probes <- mappedkeys(x)
35 
+# Convert to a list
36 
+xx <- as.list(x[mapped_probes])
37 
+if(length(xx) > 0) {
38 
+  # Get the CHR for the first five probes
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+  xx[1:5]
40 
+  # Get the first one
41 
+  xx[[1]]
42 
+}
31 43 
 }
32 44 
 \keyword{datasets}
33 45
inst/AnnDbPkg-templates/NCBICHIP.DB/man/CHRLENGTHS.Rd
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@@ -11,12 +11,24 @@
11 11
12 12 
    Total lengths of chromosomes were derived by calculating the
13 13 
    number of base pairs on the sequence string for each chromosome.
14 
+}
14 15
16 
+\seealso{
17 
+  \itemize{
18 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
19 
+          the \code{select()} interface.
20 
+  }
15 21 
 }
22 
+
16 23 
 \examples{
17 
-    tt <- @ANNOBJPREFIX@CHRLENGTHS
18 
-    # Length of chromosome 1
19 
-    tt["1"]
24 
+## select() interface:
25 
+## Objects in this package can be accessed using the select() interface
26 
+## from the AnnotationDbi package. See ?select for details.
27 
+
28 
+## Bimap interface:
29 
+tt <- @ANNOBJPREFIX@CHRLENGTHS
30 
+# Length of chromosome 1
31 
+tt["1"]
20 32 
 }
21 33 
 \keyword{datasets}
22 34
inst/AnnDbPkg-templates/NCBICHIP.DB/man/CHRLOC.Rd
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@@ -26,20 +26,32 @@
26 26 
   multiple locations.
27 27
28 28 
   Mappings were based on data provided by: @CHRLOCSOURCE@
29 
-
30 29 
 }
30 
+
31 
+\seealso{
32 
+  \itemize{
33 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
34 
+          the \code{select()} interface.
35 
+  }
36 
+}
37 
+
31 38 
 \examples{
32 
-        x <- @ANNOBJPREFIX@CHRLOC
33 
-        # Get the probe identifiers that are mapped to chromosome locations
34 
-        mapped_probes <- mappedkeys(x)
35 
-        # Convert to a list
36 
-        xx <- as.list(x[mapped_probes])
37 
-        if(length(xx) > 0) {
38 
-          # Get the CHRLOC for the first five probes
39 
-          xx[1:5]
40 
-          # Get the first one
41 
-          xx[[1]]
42 
-        }
39 
+## select() interface:
40 
+## Objects in this package can be accessed using the select() interface
41 
+## from the AnnotationDbi package. See ?select for details.
42 
+
43 
+## Bimap interface:
44 
+x <- @ANNOBJPREFIX@CHRLOC
45 
+# Get the probe identifiers that are mapped to chromosome locations
46 
+mapped_probes <- mappedkeys(x)
47 
+# Convert to a list
48 
+xx <- as.list(x[mapped_probes])
49 
+if(length(xx) > 0) {
50 
+  # Get the CHRLOC for the first five probes
51 
+  xx[1:5]
52 
+  # Get the first one
53 
+  xx[[1]]
54 
+}
43 55 
 }
44 56 
 \keyword{datasets}
45 57
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ENSEMBL.Rd
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@@ -29,27 +29,39 @@
29 29 
   mapping data at NCBI.
30 30 
 }
31 31
32 
+\seealso{
33 
+  \itemize{
34 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
35 
+          the \code{select()} interface.
36 
+  }
37 
+}
38 
+
32 39 
 \examples{
33 
-    x <- @ANNOBJPREFIX@ENSEMBL
34 
-    # Get the entrez gene IDs that are mapped to an Ensembl ID
35 
-    mapped_genes <- mappedkeys(x)
36 
-    # Convert to a list
37 
-    xx <- as.list(x[mapped_genes])
38 
-    if(length(xx) > 0) {
39 
-      # Get the Ensembl gene IDs for the first five genes
40 
-      xx[1:5]
41 
-      # Get the first one
42 
-      xx[[1]]
43 
-    }
44 
-    #For the reverse map ENSEMBL2PROBE:
45 
-    # Convert to a list
46 
-    xx <- as.list(@ANNOBJPREFIX@ENSEMBL2PROBE)
47 
-    if(length(xx) > 0){
48 
-       # Gets the entrez gene IDs for the first five Ensembl IDs
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-       xx[1:5]
50 
-       # Get the first one
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-       xx[[1]]
52 
-    }
40 
+## select() interface:
41 
+## Objects in this package can be accessed using the select() interface
42 
+## from the AnnotationDbi package. See ?select for details.
43 
+
44 
+## Bimap interface:
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+x <- @ANNOBJPREFIX@ENSEMBL
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+# Get the entrez gene IDs that are mapped to an Ensembl ID
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+mapped_genes <- mappedkeys(x)
48 
+# Convert to a list
49 
+xx <- as.list(x[mapped_genes])
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+if(length(xx) > 0) {
51 
+  # Get the Ensembl gene IDs 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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+#For the reverse map ENSEMBL2PROBE:
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+# Convert to a list
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+xx <- as.list(@ANNOBJPREFIX@ENSEMBL2PROBE)
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+if(length(xx) > 0){
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+   # Gets the entrez gene IDs for the first five Ensembl IDs
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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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+}
53 65 
 }
54 66 
 \keyword{datasets}
55 67
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ENTREZID.Rd
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@@ -7,32 +7,46 @@
7 7 
   manufacturer identifiers and Entrez Gene identifiers.
8 8 
 }
9 9 
 \details{
10 
-  Each manufacturer identifier is mapped to a vector of Entrez Gene identifiers. An
11 
-  \code{NA} is assigned to those manufacturer identifiers that can not be mapped
12 
-  to an Entrez Gene identifier at this time.
10 
+  Each manufacturer identifier is mapped to a vector of Entrez Gene
11 
+  identifiers. An \code{NA} is assigned to those manufacturer identifiers that
12 
+  can not be mapped to an Entrez Gene identifier at this time.
13 13
14 
-  If a given manufacturer identifier can be mapped to different Entrez Gene identifiers
15 
-  from various sources, we attempt to select the common identifiers. If a
16 
-  concensus cannot be determined, we select the smallest identifier.
14 
+  If a given manufacturer identifier can be mapped to different Entrez Gene
15 
+  identifiers from various sources, we attempt to select the common
16 
+  identifiers. If a concensus cannot be determined, we select the smallest
17 
+  identifier.
17 18
18 19 
   Mappings were based on data provided by: @ENTREZIDSOURCE@
19 
-
20 20 
 }
21 
+
21 22 
 \references{
22 23 
 \url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene}
23 24 
 }
25 
+
26 
+\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.
30 
+  }
31 
+}
32 
+
24 33 
 \examples{
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-        x <- @ANNOBJPREFIX@ENTREZID
26 
-        # Get the probe identifiers that are mapped to an ENTREZ Gene ID
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-        mapped_probes <- mappedkeys(x)
28 
-        # Convert to a list
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-        xx <- as.list(x[mapped_probes])
30 
-        if(length(xx) > 0) {
31 
-          # Get the ENTREZID for the first five probes
32 
-          xx[1:5]
33 
-          # Get the first one
34 
-          xx[[1]]
35 
-        }
34 
+## select() interface:
35 
+## Objects in this package can be accessed using the select() interface
36 
+## from the AnnotationDbi package. See ?select for details.
37 
+
38 
+## Bimap interface:
39 
+x <- @ANNOBJPREFIX@ENTREZID
40 
+# Get the probe identifiers that are mapped to an ENTREZ Gene ID
41 
+mapped_probes <- mappedkeys(x)
42 
+# Convert to a list
43 
+xx <- as.list(x[mapped_probes])
44 
+if(length(xx) > 0) {
45 
+  # Get the ENTREZID for the first five probes
46 
+  xx[1:5]
47 
+  # Get the first one
48 
+  xx[[1]]
49 
+}
36 50 
 }
37 51
38 52 
 \keyword{datasets}
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ENZYME.Rd
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@@ -53,31 +53,45 @@
53 53 
   provided by: @ENZYMESOURCE@
54 54
55 55 
 }
56 
+
56 57 
 \references{
57 58 
 \url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}
58 59 
 }
60 
+
61 
+\seealso{
62 
+  \itemize{
63 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
64 
+          the \code{select()} interface.
65 
+  }
66 
+}
67 
+
59 68 
 \examples{
60 
-    x <- @ANNOBJPREFIX@ENZYME
61 
-    # Get the probe identifiers that are mapped to an EC number
62 
-    mapped_probes <- mappedkeys(x)
63 
-    # Convert to a list
64 
-    xx <- as.list(x[mapped_probes])
65 
-    if(length(xx) > 0) {
66 
-      # Get the ENZYME for the first five probes
67 
-      xx[1:5]
68 
-      # Get the first one
69 
-      xx[[1]]
70 
-    }
69 
+## select() interface:
70 
+## Objects in this package can be accessed using the select() interface
71 
+## from the AnnotationDbi package. See ?select for details.
71 72
72 
-    # Now convert @ANNOBJPREFIX@ENZYME2PROBE to a list to see inside
73 
-    xx <- as.list(@ANNOBJPREFIX@ENZYME2PROBE)
74 
-    if(length(xx) > 0){
75 
-       # Get the probe identifiers for the first five enzyme
76 
-       #commission numbers
77 
-       xx[1:5]
78 
-       # Get the first one
79 
-       xx[[1]]
80 
-    }
73 
+## Bimap interface:
74 
+x <- @ANNOBJPREFIX@ENZYME
75 
+# Get the probe identifiers that are mapped to an EC number
76 
+mapped_probes <- mappedkeys(x)
77 
+# Convert to a list
78 
+xx <- as.list(x[mapped_probes])
79 
+if(length(xx) > 0) {
80 
+  # Get the ENZYME for the first five probes
81 
+  xx[1:5]
82 
+  # Get the first one
83 
+  xx[[1]]
84 
+}
85 
+
86 
+# Now convert @ANNOBJPREFIX@ENZYME2PROBE to a list to see inside
87 
+xx <- as.list(@ANNOBJPREFIX@ENZYME2PROBE)
88 
+if(length(xx) > 0){
89 
+   # Get the probe identifiers for the first five enzyme
90 
+   #commission numbers
91 
+   xx[1:5]
92 
+   # Get the first one
93 
+   xx[[1]]
94 
+}
81 95 
 }
82 96 
 \keyword{datasets}
83 97
inst/AnnDbPkg-templates/NCBICHIP.DB/man/FLYBASE.Rd
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@@ -13,29 +13,41 @@
13 13 
   Mappings were based on data provided by: @FLYBASESOURCE@
14 14 
 }
15 15
16 
+\seealso{
17 
+  \itemize{
18 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
19 
+          the \code{select()} interface.
20 
+  }
21 
+}
22 
+
16 23 
 \examples{
17 
-    x <- @ANNOBJPREFIX@FLYBASE
18 
-    # Get the manufacturer identifiers that are mapped to a FLYBASE ID
19 
-    mapped_genes <- mappedkeys(x)
20 
-    # Convert to a list
21 
-    xx <- as.list(x[mapped_genes])
22 
-    if(length(xx) > 0) {
23 
-      # Get the FlyBase IDs for the first five genes
24 
-      xx[1:5]
25 
-      # Get the first one
26 
-      xx[[1]]
27 
-    }
28 
-    # For the reverse map:
29 
-    # Convert to a list
30 
-    xx <- as.list(@ANNOBJPREFIX@FLYBASE2PROBE)
31 
-   if(length(xx) > 0){
32 
-       # Get the probe identifiers for the first five IDs
33 
-       xx[1:5]
34 
-       # Get the first one
35 
-       xx[[1]]
36 
-    }
24 
+## select() interface:
25 
+## Objects in this package can be accessed using the select() interface
26 
+## from the AnnotationDbi package. See ?select for details.
37 27
28 
+## Bimap interface:
29 
+x <- @ANNOBJPREFIX@FLYBASE
30 
+# Get the manufacturer identifiers that are mapped to a FLYBASE ID
31 
+mapped_genes <- mappedkeys(x)
32 
+# Convert to a list
33 
+xx <- as.list(x[mapped_genes])
34 
+if(length(xx) > 0) {
35 
+  # Get the FlyBase IDs for the first five genes
36 
+  xx[1:5]
37 
+  # Get the first one
38 
+  xx[[1]]
39 
+}
40 
+# For the reverse map:
41 
+# Convert to a list
42 
+xx <- as.list(@ANNOBJPREFIX@FLYBASE2PROBE)
43 
+if(length(xx) > 0){
44 
+    # Get the probe identifiers for the first five IDs
45 
+    xx[1:5]
46 
+    # Get the first one
47 
+    xx[[1]]
38 48 
 }
49 
+}
50 
+
39 51 
 \keyword{datasets}
40 52
41 53
inst/AnnDbPkg-templates/NCBICHIP.DB/man/FLYBASECG.Rd
History View file @ a92ed3e
... ... 
@@ -7,6 +7,7 @@
7 7 
   manufacturer identifiers and FlyBase CG accession numbers.  These
8 8 
   accessions are used by Ensembl and supported by FlyBase.
9 9 
 }
10 
+
10 11 
 \details{
11 12 
   This object is a simple mapping of manufacturer identifiers
12 13 
   \url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to Flybase
... ... 
@@ -15,27 +16,39 @@
15 16 
   Mappings were based on data provided by: @FLYBASESOURCE@
16 17 
 }
17 18
19 
+\seealso{
20 
+  \itemize{
21 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
22 
+          the \code{select()} interface.
23 
+  }
24 
+}
25 
+
18 26 
 \examples{
19 
-    x <- @ANNOBJPREFIX@FLYBASECG
20 
-    # Get the manufacturer IDs that are mapped to a Flybase CG ID
21 
-    mapped_genes <- mappedkeys(x)
22 
-    # Convert to a list
23 
-    xx <- as.list(x[mapped_genes])
24 
-    if(length(xx) > 0) {
25 
-      # Get the FlyBase CG IDs for the first five genes
26 
-      xx[1:5]
27 
-      # Get the first one
28 
-      xx[[1]]
29 
-    }
30 
-    #For the reverse map FLYBASECG2EG:
31 
-    # Convert to a list
32 
-    xx <- as.list(@ANNOBJPREFIX@FLYBASECG2PROBE)
33 
-    if(length(xx) > 0){
34 
-       # Gets the manufacturer IDs for the first five FlyBase CG IDs
35 
-       xx[1:5]
36 
-       # Get the first one
37 
-       xx[[1]]
38 
-    }
27 
+## select() interface:
28 
+## Objects in this package can be accessed using the select() interface
29 
+## from the AnnotationDbi package. See ?select for details.
30 
+
31 
+## Bimap interface:
32 
+x <- @ANNOBJPREFIX@FLYBASECG
33 
+# Get the manufacturer IDs that are mapped to a Flybase CG ID
34 
+mapped_genes <- mappedkeys(x)
35 
+# Convert to a list
36 
+xx <- as.list(x[mapped_genes])
37 
+if(length(xx) > 0) {
38 
+  # Get the FlyBase CG IDs for the first five genes
39 
+  xx[1:5]
40 
+  # Get the first one
41 
+  xx[[1]]
42 
+}
43 
+#For the reverse map FLYBASECG2EG:
44 
+# Convert to a list
45 
+xx <- as.list(@ANNOBJPREFIX@FLYBASECG2PROBE)
46 
+if(length(xx) > 0){
47 
+   # Gets the manufacturer IDs for the first five FlyBase CG IDs
48 
+   xx[1:5]
49 
+   # Get the first one
50 
+   xx[[1]]
51 
+}
39 52 
 }
40 53 
 \keyword{datasets}
41 54
inst/AnnDbPkg-templates/NCBICHIP.DB/man/GENENAME.Rd
History View file @ a92ed3e
... ... 
@@ -19,18 +19,30 @@
19 19
20 20 
 }
21 21
22 
+\seealso{
23 
+  \itemize{
24 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
25 
+          the \code{select()} interface.
26 
+  }
27 
+}
28 
+
22 29 
 \examples{
23 
-        x <- @ANNOBJPREFIX@GENENAME
24 
-        # Get the probe identifiers that are mapped to a gene name
25 
-        mapped_probes <- mappedkeys(x)
26 
-        # Convert to a list
27 
-        xx <- as.list(x[mapped_probes])
28 
-        if(length(xx) > 0) {
29 
-          # Get the GENENAME for the first five probes
30 
-          xx[1:5]
31 
-          # Get the first one
32 
-          xx[[1]]
33 
-        }
30 
+## select() interface:
31 
+## Objects in this package can be accessed using the select() interface
32 
+## from the AnnotationDbi package. See ?select for details.
33 
+
34 
+## Bimap interface:
35 
+x <- @ANNOBJPREFIX@GENENAME
36 
+# Get the probe identifiers that are mapped to a gene name
37 
+mapped_probes <- mappedkeys(x)
38 
+# Convert to a list
39 
+xx <- as.list(x[mapped_probes])
40 
+if(length(xx) > 0) {
41 
+  # Get the GENENAME for the first five probes
42 
+  xx[1:5]
43 
+  # Get the first one
44 
+  xx[[1]]
45 
+}
34 46 
 }
35 47 
 \keyword{datasets}
36 48
inst/AnnDbPkg-templates/NCBICHIP.DB/man/GO.Rd
History View file @ a92ed3e
... ... 
@@ -81,45 +81,58 @@
81 81
82 82 
   All mappings were based on data provided by: @GOSOURCE@
83 83 
 }
84 
-\seealso{
85 
-  \code{\link{@ANNOBJPREFIX@GO2ALLPROBES}}.
86 
-}
84 
+
87 85 
 \references{
88 86 
 \url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/}
89 87 
 }
88 
+
89 
+\seealso{
90 
+  \itemize{
91 
+    \item \code{\link{@ANNOBJPREFIX@GO2ALLPROBES}}
92 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
93 
+          the \code{select()} interface.
94 
+  }
95 
+}
96 
+
90 97 
 \examples{
91 
-    x <- @ANNOBJPREFIX@GO
92 
-    # Get the manufacturer identifiers that are mapped to a GO ID
93 
-    mapped_genes <- mappedkeys(x)
94 
-    # Convert to a list
95 
-    xx <- as.list(x[mapped_genes])
96 
-    if(length(xx) > 0) {
97 
-        # Try the first one
98 
-        got <- xx[[1]]
99 
-        got[[1]][["GOID"]]
100 
-        got[[1]][["Ontology"]]
101 
-        got[[1]][["Evidence"]]
102 
-    }
103 
-    # For the reverse map:
104 
-    # Convert to a list
105 
-    xx <- as.list(@ANNOBJPREFIX@GO2PROBE)
106 
-    if(length(xx) > 0){
107 
-        # Gets the manufacturer ids for the top 2nd and 3nd GO identifiers
108 
-        goids <- xx[2:3]
109 
-        # Gets the manufacturer ids for the first element of goids
110 
-        goids[[1]]
111 
-        # Evidence code for the mappings
112 
-        names(goids[[1]])
113 
-    }
114 
-    # Convert @ANNOBJPREFIX@GO2ALLPROBES to a list
115 
-    xx <- as.list(@ANNOBJPREFIX@GO2ALLPROBES)
116 
-    if(length(xx) > 0){
117 
-        # Gets the manufacturer identifiers for the top 2nd and 3nd GO identifiers
118 
-        goids <- xx[2:3]
119 
-        # Gets all the manufacturer identifiers for the first element of goids
120 
-        goids[[1]]
121 
-        # Evidence code for the mappings
122 
-        names(goids[[1]])
123 
-    }
98 
+## select() interface:
99 
+## Objects in this package can be accessed using the select() interface
100 
+## from the AnnotationDbi package. See ?select for details.
101 
+
102 
+## Bimap interface:
103 
+x <- @ANNOBJPREFIX@GO
104 
+# Get the manufacturer identifiers that are mapped to a GO ID
105 
+mapped_genes <- mappedkeys(x)
106 
+# Convert to a list
107 
+xx <- as.list(x[mapped_genes])
108 
+if(length(xx) > 0) {
109 
+    # Try the first one
110 
+    got <- xx[[1]]
111 
+    got[[1]][["GOID"]]
112 
+    got[[1]][["Ontology"]]
113 
+    got[[1]][["Evidence"]]
114 
+}
115 
+# For the reverse map:
116 
+# Convert to a list
117 
+xx <- as.list(@ANNOBJPREFIX@GO2PROBE)
118 
+if(length(xx) > 0){
119 
+    # Gets the manufacturer ids for the top 2nd and 3nd GO identifiers
120 
+    goids <- xx[2:3]
121 
+    # Gets the manufacturer ids for the first element of goids
122 
+    goids[[1]]
123 
+    # Evidence code for the mappings
124 
+    names(goids[[1]])
125 
+}
126 
+# Convert @ANNOBJPREFIX@GO2ALLPROBES to a list
127 
+xx <- as.list(@ANNOBJPREFIX@GO2ALLPROBES)
128 
+if(length(xx) > 0){
129 
+# Gets the manufacturer identifiers for the top 2nd and 3nd GO identifiers
130 
+    goids <- xx[2:3]
131 
+    # Gets all the manufacturer identifiers for the first element of goids
132 
+    goids[[1]]
133 
+    # Evidence code for the mappings
134 
+    names(goids[[1]])
124 135 
 }
136 
+}
137 
+
125 138 
 \keyword{datasets}
inst/AnnDbPkg-templates/NCBICHIP.DB/man/MAP.Rd
History View file @ a92ed3e
... ... 
@@ -22,21 +22,35 @@
22 22 
   Mappings were based on data provided by: @MAPSOURCE@
23 23
24 24 
 }
25 
+
25 26 
 \references{
26 27 
   \url{http://www.ncbi.nlm.nih.gov}
27 28 
 }
29 
+
30 
+\seealso{
31 
+  \itemize{
32 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
33 
+          the \code{select()} interface.
34 
+  }
35 
+}
36 
+
28 37 
 \examples{
29 
-        x <- @ANNOBJPREFIX@MAP
30 
-        # Get the probe identifiers that are mapped to any cytoband
31 
-        mapped_probes <- mappedkeys(x)
32 
-        # Convert to a list
33 
-        xx <- as.list(x[mapped_probes])
34 
-        if(length(xx) > 0) {
35 
-          # Get the MAP for the first five probes
36 
-          xx[1:5]
37 
-          # Get the first one
38 
-          xx[[1]]
39 
-        }
38 
+## select() interface:
39 
+## Objects in this package can be accessed using the select() interface
40 
+## from the AnnotationDbi package. See ?select for details.
41 
+
42 
+## Bimap interface:
43 
+x <- @ANNOBJPREFIX@MAP
44 
+# Get the probe identifiers that are mapped to any cytoband
45 
+mapped_probes <- mappedkeys(x)
46 
+# Convert to a list
47 
+xx <- as.list(x[mapped_probes])
48 
+if(length(xx) > 0) {
49 
+  # Get the MAP for the first five probes
50 
+  xx[1:5]
51 
+  # Get the first one
52 
+  xx[[1]]
53 
+}
40 54 
 }
41 55 
 \keyword{datasets}
42 56
inst/AnnDbPkg-templates/NCBICHIP.DB/man/MAPCOUNTS.Rd
History View file @ a92ed3e
... ... 
@@ -21,21 +21,30 @@
21 21 
 }
22 22
23 23 
 \seealso{
24 
-  \code{\link[AnnotationDbi:Bimap-keys]{mappedkeys}},
25 
-  \code{\link[AnnotationDbi:Bimap-keys]{count.mappedkeys}},
26 
-  \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}}
24 
+  \itemize{
25 
+    \item \code{\link[AnnotationDbi:Bimap-keys]{mappedkeys}}
26 
+    \item \code{\link[AnnotationDbi:Bimap-keys]{count.mappedkeys}}
27 
+    \item \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}}
28 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
29 
+          the \code{select()} interface.
30 
+  }
27 31 
 }
28 32
29 33 
 \examples{
30 
-  @ANNOBJPREFIX@MAPCOUNTS
31 
-  mapnames <- names(@ANNOBJPREFIX@MAPCOUNTS)
32 
-  @ANNOBJPREFIX@MAPCOUNTS[mapnames[1]]
33 
-  x <- get(mapnames[1])
34 
-  sum(!is.na(as.list(x)))
35 
-  count.mappedkeys(x)   # much faster!
36 
-
37 
-  ## Check the "map count" of all the maps in package @PKGNAME@
38 
-  checkMAPCOUNTS("@PKGNAME@")
34 
+## select() interface:
35 
+## Objects in this package can be accessed using the select() interface
36 
+## from the AnnotationDbi package. See ?select for details.
37 
+
38 
+## Bimap interface:
39 
+@ANNOBJPREFIX@MAPCOUNTS
40 
+mapnames <- names(@ANNOBJPREFIX@MAPCOUNTS)
41 
+@ANNOBJPREFIX@MAPCOUNTS[mapnames[1]]
42 
+x <- get(mapnames[1])
43 
+sum(!is.na(as.list(x)))
44 
+count.mappedkeys(x)   # much faster!
45 
+
46 
+## Check the "map count" of all the maps in package @PKGNAME@
47 
+checkMAPCOUNTS("@PKGNAME@")
39 48 
 }
40 49
41 50 
 \keyword{datasets}
inst/AnnDbPkg-templates/NCBICHIP.DB/man/MGI.Rd
History View file @ a92ed3e
... ... 
@@ -13,27 +13,39 @@
13 13 
   Mappings were based on data provided by: @MGISOURCE@
14 14 
 }
15 15
16 
+\seealso{
17 
+  \itemize{
18 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
19 
+          the \code{select()} interface.
20 
+  }
21 
+}
22 
+
16 23 
 \examples{
17 
-    x <- @ANNOBJPREFIX@MGI
18 
-    # Get the manufacturer IDs that are mapped to an MGI ID
19 
-    mapped_genes <- mappedkeys(x)
20 
-    # Convert to a list
21 
-    xx <- as.list(x[mapped_genes])
22 
-    if(length(xx) > 0) {
23 
-      # Get the MGI IDs for the first five genes
24 
-      xx[1:5]
25 
-      # Get the first one
26 
-      xx[[1]]
27 
-    }
28 
-    #For the reverse map MGI2EG:
29 
-    # Convert to a list
30 
-    xx <- as.list(@ANNOBJPREFIX@MGI2PROBE)
31 
-    if(length(xx) > 0){
32 
-       # Gets the manufacturer IDs for the first five MGI IDs
33 
-       xx[1:5]
34 
-       # Get the first one
35 
-       xx[[1]]
36 
-    }
24 
+## select() interface:
25 
+## Objects in this package can be accessed using the select() interface
26 
+## from the AnnotationDbi package. See ?select for details.
27 
+
28 
+## Bimap interface:
29 
+x <- @ANNOBJPREFIX@MGI
30 
+# Get the manufacturer IDs that are mapped to an MGI ID
31 
+mapped_genes <- mappedkeys(x)
32 
+# Convert to a list
33 
+xx <- as.list(x[mapped_genes])
34 
+if(length(xx) > 0) {
35 
+  # Get the MGI IDs for the first five genes
36 
+  xx[1:5]
37 
+  # Get the first one
38 
+  xx[[1]]
39 
+}
40 
+#For the reverse map MGI2EG:
41 
+# Convert to a list
42 
+xx <- as.list(@ANNOBJPREFIX@MGI2PROBE)
43 
+if(length(xx) > 0){
44 
+   # Gets the manufacturer IDs for the first five MGI IDs
45 
+   xx[1:5]
46 
+   # Get the first one
47 
+   xx[[1]]
48 
+}
37 49 
 }
38 50 
 \keyword{datasets}
39 51
inst/AnnDbPkg-templates/NCBICHIP.DB/man/OMIM.Rd
History View file @ a92ed3e
... ... 
@@ -7,36 +7,49 @@
7 7 
   manufacturer identifiers and OMIM identifiers.
8 8 
 }
9 9 
 \details{
10 
-  Each manufacturer identifier is mapped to a vector of OMIM identifiers. The vector
11 
-  length may be one or longer, depending on how many OMIM identifiers the
12 
-  manufacturer identifier maps to. An \code{NA} is reported for any manufacturer
13 
-  identifier that cannot be mapped to an OMIM identifier at this time.
10 
+  Each manufacturer identifier is mapped to a vector of OMIM identifiers. The
11 
+  vector length may be one or longer, depending on how many OMIM identifiers
12 
+  the manufacturer identifier maps to. An \code{NA} is reported for any
13 
+  manufacturer identifier that cannot be mapped to an OMIM identifier at this
14 
+  time.
14 15
15 
-  OMIM is based upon the book Mendelian Inheritance in Man
16 
-  (V. A. McKusick) and focuses primarily on inherited or heritable
17 
-  genetic diseases. It contains textual information, pictures, and reference
18 
-  information that can be searched using various terms, among which the
19 
-  MIM number is one.
16 
+  OMIM is based upon the book Mendelian Inheritance in Man (V. A. McKusick) and
17 
+  focuses primarily on inherited or heritable genetic diseases. It contains
18 
+  textual information, pictures, and reference information that can be searched
19 
+  using various terms, among which the MIM number is one.
20 20
21 21 
   Mappings were based on data provided by: @OMIMSOURCE@
22 
-
23 22 
 }
23 
+
24 24 
 \references{
25 25 
   \url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene}
26 26 
   \url{http://www3.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM}
27 27 
 }
28 
+
29 
+\seealso{
30 
+  \itemize{
31 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
32 
+          the \code{select()} interface.
33 
+  }
34 
+}
35 
+
28 36 
 \examples{
29 
-        x <- @ANNOBJPREFIX@OMIM
30 
-        # Get the probe identifiers that are mapped to a OMIM ID
31 
-        mapped_probes <- mappedkeys(x)
32 
-        # Convert to a list
33 
-        xx <- as.list(x[mapped_probes])
34 
-        if(length(xx) > 0) {
35 
-          # Get the OMIM for the first five probes
36 
-          xx[1:5]
37 
-          # Get the first one
38 
-          xx[[1]]
39 
-        }
37 
+## select() interface:
38 
+## Objects in this package can be accessed using the select() interface
39 
+## from the AnnotationDbi package. See ?select for details.
40 
+
41 
+## Bimap interface:
42 
+x <- @ANNOBJPREFIX@OMIM
43 
+# Get the probe identifiers that are mapped to a OMIM ID
44 
+mapped_probes <- mappedkeys(x)
45 
+# Convert to a list
46 
+xx <- as.list(x[mapped_probes])
47 
+if(length(xx) > 0) {
48 
+  # Get the OMIM for the first five probes
49 
+  xx[1:5]
50 
+  # Get the first one
51 
+  xx[[1]]
52 
+}
40 53 
 }
41 54
42 55 
 \keyword{datasets}
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ORGANISM.Rd
History View file @ a92ed3e
... ... 
@@ -23,9 +23,23 @@
23 23 
   most programatic acces will not require this extension, so its more
24 24 
   convenient to leave it out.
25 25 
 }
26 
+
27 
+\seealso{
28 
+  \itemize{
29 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
30 
+          the \code{select()} interface.
31 
+  }
32 
+}
33 
+
26 34 
 \examples{
27 
-  @ANNOBJPREFIX@ORGANISM
28 
-  @ANNOBJPREFIX@ORGPKG
35 
+## select() interface:
36 
+## Objects in this package can be accessed using the select() interface
37 
+## from the AnnotationDbi package. See ?select for details.
38 
+
39 
+## Bimap interface:
40 
+@ANNOBJPREFIX@ORGANISM
41 
+@ANNOBJPREFIX@ORGPKG
29 42 
 }
43 
+
30 44 
 \keyword{datasets}
31 45
inst/AnnDbPkg-templates/NCBICHIP.DB/man/PATH.Rd
History View file @ a92ed3e
... ... 
@@ -26,30 +26,44 @@
26 26 
   Mappings were based on data provided by: @PATHSOURCE@
27 27
28 28 
 }
29 
+
29 30 
 \references{
30 31 
   \url{http://www.genome.ad.jp/kegg/}
31 32 
 }
33 
+
34 
+\seealso{
35 
+  \itemize{
36 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
37 
+          the \code{select()} interface.
38 
+  }
39 
+}
40 
+
32 41 
 \examples{
33 
-    x <- @ANNOBJPREFIX@PATH
34 
-    # Get the probe identifiers that are mapped to a KEGG pathway ID
35 
-    mapped_probes <- mappedkeys(x)
36 
-    # Convert to a list
37 
-    xx <- as.list(x[mapped_probes])
38 
-    if(length(xx) > 0) {
39 
-      # Get the PATH for the first five probes
40 
-      xx[1:5]
41 
-      # Get the first one
42 
-      xx[[1]]
43 
-    }
44 
-
45 
-    # Now convert the @ANNOBJPREFIX@PATH2PROBE object to a list
46 
-    xx <- as.list(@ANNOBJPREFIX@PATH2PROBE)
47 
-    if(length(xx) > 0){
48 
-        # Get the probe identifiers for the first two pathway identifiers
49 
-        xx[1:2]
50 
-        # Get the first one
51 
-        xx[[1]]
52 
-    }
42 
+## select() interface:
43 
+## Objects in this package can be accessed using the select() interface
44 
+## from the AnnotationDbi package. See ?select for details.
45 
+
46 
+## Bimap interface:
47 
+x <- @ANNOBJPREFIX@PATH
48 
+# Get the probe identifiers that are mapped to a KEGG pathway ID
49 
+mapped_probes <- mappedkeys(x)
50 
+# Convert to a list
51 
+xx <- as.list(x[mapped_probes])
52 
+if(length(xx) > 0) {
53 
+  # Get the PATH for the first five probes
54 
+  xx[1:5]
55 
+  # Get the first one
56 
+  xx[[1]]
57 
+}
58 
+
59 
+# Now convert the @ANNOBJPREFIX@PATH2PROBE object to a list
60 
+xx <- as.list(@ANNOBJPREFIX@PATH2PROBE)
61 
+if(length(xx) > 0){
62 
+    # Get the probe identifiers for the first two pathway identifiers
63 
+    xx[1:2]
64 
+    # Get the first one
65 
+    xx[[1]]
66 
+}
53 67 
 }
54 68 
 \keyword{datasets}
55 69
inst/AnnDbPkg-templates/NCBICHIP.DB/man/PMID.Rd
History View file @ a92ed3e
... ... 
@@ -32,43 +32,58 @@
32 32 
   Mappings were based on data provided by: @PMIDSOURCE@
33 33
34 34 
 }
35 
+
35 36 
 \references{
36 37 
   \url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed}
37 38 
 }
39 
+
40 
+\seealso{
41 
+  \itemize{
42 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
43 
+          the \code{select()} interface.
44 
+  }
45 
+}
46 
+
38 47 
 \examples{
39 
-        x <- @ANNOBJPREFIX@PMID
40 
-        # Get the probe identifiers that are mapped to any PubMed ID
41 
-        mapped_probes <- mappedkeys(x)
42 
-        # Convert to a list
43 
-        xx <- as.list(x[mapped_probes])
44 
-    if(length(xx) > 0){
45 
-        # Get the PubMed identifiers for the first two probe identifiers
46 
-        xx[1:2]
47 
-        # Get the first one
48 
-        xx[[1]]
49 
-        if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]])
50 
-           && require(annotate)){
51 
-            # Get article information as XML files
52 
-            xmls <- pubmed(xx[[1]], disp = "data")
53 
-            # View article information using a browser
54 
-            pubmed(xx[[1]], disp = "browser")
55 
-        }
48 
+## select() interface:
49 
+## Objects in this package can be accessed using the select() interface
50 
+## from the AnnotationDbi package. See ?select for details.
51 
+
52 
+## Bimap interface:
53 
+x <- @ANNOBJPREFIX@PMID
54 
+# Get the probe identifiers that are mapped to any PubMed ID
55 
+mapped_probes <- mappedkeys(x)
56 
+# Convert to a list
57 
+xx <- as.list(x[mapped_probes])
58 
+if(length(xx) > 0){
59 
+    # Get the PubMed identifiers for the first two probe identifiers
60 
+    xx[1:2]
61 
+    # Get the first one
62 
+    xx[[1]]
63 
+    if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]])
64 
+       && require(annotate)){
65 
+        # Get article information as XML files
66 
+        xmls <- pubmed(xx[[1]], disp = "data")
67 
+        # View article information using a browser
68 
+        pubmed(xx[[1]], disp = "browser")
56 69 
     }
70 
+}
57 71
58 
-    # Now convert the reverse map object @ANNOBJPREFIX@PMID2PROBE to a list
59 
-    xx <- as.list(@ANNOBJPREFIX@PMID2PROBE)
60 
-    if(length(xx) > 0){
61 
-        # Get the probe identifiers for the first two PubMed identifiers
62 
-        xx[1:2]
63 
-        # Get the first one
64 
-        xx[[1]]
65 
-        if(interactive() && require(annotate)){
66 
-            # Get article information as XML files for a PubMed id
67 
-            xmls <- pubmed(names(xx)[1], disp = "data")
68 
-            # View article information using a browser
69 
-            pubmed(names(xx)[1], disp = "browser")
70 
-        }
72 
+# Now convert the reverse map object @ANNOBJPREFIX@PMID2PROBE to a list
73 
+xx <- as.list(@ANNOBJPREFIX@PMID2PROBE)
74 
+if(length(xx) > 0){
75 
+    # Get the probe identifiers for the first two PubMed identifiers
76 
+    xx[1:2]
77 
+    # Get the first one
78 
+    xx[[1]]
79 
+    if(interactive() && require(annotate)){
80 
+        # Get article information as XML files for a PubMed id
81 
+        xmls <- pubmed(names(xx)[1], disp = "data")
82 
+        # View article information using a browser
83 
+        pubmed(names(xx)[1], disp = "browser")
71 84 
     }
72 85 
 }
86 
+}
87 
+
73 88 
 \keyword{datasets}
74 89
inst/AnnDbPkg-templates/NCBICHIP.DB/man/REFSEQ.Rd
History View file @ a92ed3e
... ... 
@@ -39,22 +39,36 @@
39 39 
   Mappings were based on data provided by: @REFSEQSOURCE@
40 40
41 41 
 }
42 
+
42 43 
 \references{
43 44 
     \url{http://www.ncbi.nlm.nih.gov}
44 45 
     \url{http://www.ncbi.nlm.nih.gov/RefSeq/}
45 46 
 }
47 
+
48 
+\seealso{
49 
+  \itemize{
50 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
51 
+          the \code{select()} interface.
52 
+  }
53 
+}
54 
+
46 55 
 \examples{
47 
-        x <- @ANNOBJPREFIX@REFSEQ
48 
-        # Get the probe identifiers that are mapped to any RefSeq ID
49 
-        mapped_probes <- mappedkeys(x)
50 
-        # Convert to a list
51 
-        xx <- as.list(x[mapped_probes])
52 
-        if(length(xx) > 0) {
53 
-          # Get the REFSEQ for the first five probes
54 
-          xx[1:5]
55 
-          # Get the first one
56 
-          xx[[1]]
57 
-        }
56 
+## select() interface:
57 
+## Objects in this package can be accessed using the select() interface
58 
+## from the AnnotationDbi package. See ?select for details.
59 
+
60 
+## Bimap interface:
61 
+x <- @ANNOBJPREFIX@REFSEQ
62 
+# Get the probe identifiers that are mapped to any RefSeq ID
63 
+mapped_probes <- mappedkeys(x)
64 
+# Convert to a list
65 
+xx <- as.list(x[mapped_probes])
66 
+if(length(xx) > 0) {
67 
+  # Get the REFSEQ for the first five probes
68 
+  xx[1:5]
69 
+  # Get the first one
70 
+  xx[[1]]
71 
+}
58 72 
 }
59 73
60 74 
 \keyword{datasets}
inst/AnnDbPkg-templates/NCBICHIP.DB/man/SYMBOL.Rd
History View file @ a92ed3e
... ... 
@@ -17,21 +17,35 @@
17 17 
   Mappings were based on data provided by: @SYMBOLSOURCE@
18 18
19 19 
 }
20 
+
20 21 
 \references{
21 22 
   \url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene}
22 23 
 }
24 
+
25 
+\seealso{
26 
+  \itemize{
27 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
28 
+          the \code{select()} interface.
29 
+  }
30 
+}
31 
+
23 32 
 \examples{
24 
-        x <- @ANNOBJPREFIX@SYMBOL
25 
-        # Get the probe identifiers that are mapped to a gene symbol
26 
-        mapped_probes <- mappedkeys(x)
27 
-        # Convert to a list
28 
-        xx <- as.list(x[mapped_probes])
29 
-        if(length(xx) > 0) {
30 
-          # Get the SYMBOL for the first five probes
31 
-          xx[1:5]
32 
-          # Get the first one
33 
-          xx[[1]]
34 
-        }
33 
+## select() interface:
34 
+## Objects in this package can be accessed using the select() interface
35 
+## from the AnnotationDbi package. See ?select for details.
36 
+
37 
+## Bimap interface:
38 
+x <- @ANNOBJPREFIX@SYMBOL
39 
+# Get the probe identifiers that are mapped to a gene symbol
40 
+mapped_probes <- mappedkeys(x)
41 
+# Convert to a list
42 
+xx <- as.list(x[mapped_probes])
43 
+if(length(xx) > 0) {
44 
+  # Get the SYMBOL for the first five probes
45 
+  xx[1:5]
46 
+  # Get the first one
47 
+  xx[[1]]
48 
+}
35 49 
 }
36 50
37 51 
 \keyword{datasets}
inst/AnnDbPkg-templates/NCBICHIP.DB/man/UNIGENE.Rd
History View file @ a92ed3e
... ... 
@@ -6,32 +6,45 @@
6 6 
    manufacturer identifiers and UniGene identifiers.
7 7 
 }
8 8 
 \details{
9 
-  Each manufacturer identifier is mapped to a UniGene identifier. An \code{NA} is
10 
-  reported if the manufacturer identifier cannot be mapped to UniGene at this time.
9 
+  Each manufacturer identifier is mapped to a UniGene identifier. An \code{NA}
10 
+  is reported if the manufacturer identifier cannot be mapped to UniGene at
11 
+  this time.
11 12
12 13 
   A UniGene identifier represents a cluster of sequences of a gene. Using
13 14 
   UniGene identifiers one can query the UniGene database for information about
14 
-  the sequences or the Entrez Gene database for information about the
15 
-  genes.
15 
+  the sequences or the Entrez Gene database for information about the genes.
16 16
17 17 
   Mappings were based on data provided by: @UNIGENESOURCE@
18 
-
19 18 
 }
19 
+
20 20 
 \references{
21 21 
   \url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene}
22 22 
 }
23 
+
24 
+\seealso{
25 
+  \itemize{
26 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
27 
+          the \code{select()} interface.
28 
+  }
29 
+}
30 
+
23 31 
 \examples{
24 
-        x <- @ANNOBJPREFIX@UNIGENE
25 
-        # Get the probe identifiers that are mapped to an UNIGENE ID
26 
-        mapped_probes <- mappedkeys(x)
27 
-        # Convert to a list
28 
-        xx <- as.list(x[mapped_probes])
29 
-        if(length(xx) > 0) {
30 
-          # Get the UNIGENE for the first five probes
31 
-          xx[1:5]
32 
-          # Get the first one
33 
-          xx[[1]]
34 
-        }
32 
+## select() interface:
33 
+## Objects in this package can be accessed using the select() interface
34 
+## from the AnnotationDbi package. See ?select for details.
35 
+
36 
+## Bimap interface:
37 
+x <- @ANNOBJPREFIX@UNIGENE
38 
+# Get the probe identifiers that are mapped to an UNIGENE ID
39 
+mapped_probes <- mappedkeys(x)
40 
+# Convert to a list
41 
+xx <- as.list(x[mapped_probes])
42 
+if(length(xx) > 0) {
43 
+  # Get the UNIGENE for the first five probes
44 
+  xx[1:5]
45 
+  # Get the first one
46 
+  xx[[1]]
47 
+}
35 48 
 }
36 49
37 50 
 \keyword{datasets}
inst/AnnDbPkg-templates/NCBICHIP.DB/man/UNIPROT.Rd
History View file @ a92ed3e
... ... 
@@ -15,18 +15,30 @@
15 15 
   \url{http://www.ensembl.org/biomart/martview/}
16 16 
 }
17 17
18 
+\seealso{
19 
+  \itemize{
20 
+    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
21 
+          the \code{select()} interface.
22 
+  }
23 
+}
24 
+
18 25 
 \examples{
19 
-    x <- @ANNOBJPREFIX@UNIPROT
20 
-    # Get the entrez gene IDs that are mapped to an Uniprot ID
21 
-    mapped_genes <- mappedkeys(x)
22 
-    # Convert to a list
23 
-    xx <- as.list(x[mapped_genes])
24 
-    if(length(xx) > 0) {
25 
-      # Get the Uniprot IDs for the first five genes
26 
-      xx[1:5]
27 
-      # Get the first one
28 
-      xx[[1]]
29 
-    }
26 
+## select() interface:
27 
+## Objects in this package can be accessed using the select() interface
28 
+## from the AnnotationDbi package. See ?select for details.