The Organism information for indac

Description

indacORGANISM is an R object that contains a single item: a character string that names the organism for which indac was built. indacORGPKG 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, indacORGANISM provides a simple way to programmatically extract the organism name. indacORGPKG 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.

See Also

• AnnotationDb-class for use of the 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:
indacORGANISM
indacORGPKG

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(indac.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.Dm.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/indac.db/indacORGANISM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: indacORGANISM
> ### Title: The Organism information for indac
> ### Aliases: indacORGANISM indacORGPKG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## select() interface:
> ## Objects in this package can be accessed using the select() interface
> ## from the AnnotationDbi package. See ?select for details.
> 
> ## Bimap interface:
> indacORGANISM
[1] "Drosophila melanogaster"
> indacORGPKG
[1] "org.Dm.eg"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>