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
Showing1 changed files
... ...
@@ -22,20 +22,34 @@
22 22
   Mappings were based on data provided by: @PATH2PROBESOURCE@
23 23
 
24 24
 }
25
+
25 26
 \references{
26 27
 \url{http://www.genome.ad.jp/kegg/}
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
-    # Convert the object to a list
30
-    xx <- as.list(@ANNOBJPREFIX@PATH2PROBE)
31
-    # Remove pathway identifiers that do not map to any probe id
32
-    xx <- xx[!is.na(xx)]
33
-    if(length(xx) > 0){
34
-        # The probe identifiers for the first two elements of XX
35
-        xx[1:2]
36
-        # Get the first one
37
-        xx[[1]]
38
-    } 
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
+# Convert the object to a list
44
+xx <- as.list(@ANNOBJPREFIX@PATH2PROBE)
45
+# Remove pathway identifiers that do not map to any probe id
46
+xx <- xx[!is.na(xx)]
47
+if(length(xx) > 0){
48
+    # The probe identifiers for the first two elements of XX
49
+    xx[1:2]
50
+    # Get the first one
51
+    xx[[1]]
52
+} 
39 53
 }
40 54
 
41 55
 \keyword{datasets}
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
1 1
new file mode 100644
... ...
@@ -0,0 +1,42 @@
1
+\name{@ANNOBJPREFIX@PATH2PROBE}
2
+\alias{@ANNOBJPREFIX@PATH2PROBE}
3
+\title{Map between Kyoto Encyclopedia of Genes and Genomes (KEGG)
4
+  pathway identifiers and Manufacturer Identifiers}
5
+\description{
6
+ @ANNOBJPREFIX@PATH2PROBE is an R object that provides mappings between
7
+ KEGG identifiers and manufacturer identifiers.
8
+}
9
+\details{
10
+  Each KEGG identifier is mapped to a named vector of manufacturer identifiers. The name
11
+  represents the KEGG identifier and the vector contains all manufacturer identifiers
12
+  that are found in that particular pathway. An \code{NA} is reported
13
+  for any KEGG identifier that cannot be mapped to any manufacturer identifiers.
14
+
15
+  Pathway name for a given pathway identifier can be obtained using the KEGG
16
+  data package that can either be built using AnnBuilder or downloaded
17
+  from Bioconductor \url{http://www.bioconductor.org}.
18
+
19
+  Graphic presentations of pathways are searchable at
20
+  \url{http://www.genome.ad.jp/kegg/pathway.html} using pathway identifiers as keys.
21
+  
22
+  Mappings were based on data provided by: @PATH2PROBESOURCE@
23
+
24
+}
25
+\references{
26
+\url{http://www.genome.ad.jp/kegg/}
27
+}
28
+\examples{
29
+    # Convert the object to a list
30
+    xx <- as.list(@ANNOBJPREFIX@PATH2PROBE)
31
+    # Remove pathway identifiers that do not map to any probe id
32
+    xx <- xx[!is.na(xx)]
33
+    if(length(xx) > 0){
34
+        # The probe identifiers for the first two elements of XX
35
+        xx[1:2]
36
+        # Get the first one
37
+        xx[[1]]
38
+    } 
39
+}
40
+
41
+\keyword{datasets}
42
+