lumiMouseAllORGANISM is an R object that contains a single item: a
character string that names the organism for which lumiMouseAll was
built.
lumiMouseAllORGPKG is an R object that contains a chararcter vector
with the name of the organism package that a chip package depends on
for its gene-centric annotation.
Details
Although the package name is suggestive of the organism for which it
was built, lumiMouseAllORGANISM provides a simple way to programmatically
extract the organism name.
lumiMouseAllORGPKG provides a simple way to programmatically
extract the name of the parent organism package. The parent organism
package is a strict dependency for chip packages as this is where the
gene cetric information is ultimately extracted from. The full
package name will always be this string plus the extension ".db". But
most programatic acces will not require this extension, so its more
convenient to leave it out.
Examples
lumiMouseAllORGANISM
lumiMouseAllORGPKG
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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> library(lumiMouseAll.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: org.Mm.eg.db
lumiMouseAll.db is using or is likely to need access to special nuID
identifiers. Users can learn about these identifiers from vignette
documentation provided with the lumi package.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumiMouseAll.db/lumiMouseAllORGANISM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiMouseAllORGANISM
> ### Title: The Organism information for lumiMouseAll
> ### Aliases: lumiMouseAllORGANISM lumiMouseAllORGPKG
> ### Keywords: datasets
>
> ### ** Examples
>
> lumiMouseAllORGANISM
[1] "Mus musculus"
> lumiMouseAllORGPKG
[1] "org.Mm.eg"
>
>
>
>
>
> dev.off()
null device
1
>