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

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}

#### 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.

 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 +