An annotation data file that maps Open Reading Frame (ORF) identifiers to textural descriptions of the corresponding genes

Description

org.Sc.sgdDESCRIPTION maps yeast ORF identifiers to descriptive information about genes corresponding to the ORF identifiers

Details

This is an R object containing key and value pairs. Keys are ORF identifiers and values are the corresponding descriptions of genes. Values are vectors of length 1. Probe identifiers that can not be mapped to descriptive information are assigned a value NA.

Annotation based on data provided by: Yeast Genome http://downloads.yeastgenome.org/ With a date stamp from the source of: 12-Mar-2016

References

http://www.yeastgenome.org/DownloadContents.shtml

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:
x <- org.Sc.sgdDESCRIPTION
# Get the probe identifiers that are mapped to gene descriptions
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
  # Get the gene descriptions for the first five probes
  xx[1:5]
  # For the first probe
  xx[[1]]
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(org.Sc.sgd.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


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/org.Sc.sgd.db/org.Sc.sgdDESCRIPTION.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.Sc.sgdDESCRIPTION
> ### Title: An annotation data file that maps Open Reading Frame (ORF)
> ###   identifiers to textural descriptions of the corresponding genes
> ### Aliases: org.Sc.sgdDESCRIPTION
> ### 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:
> x <- org.Sc.sgdDESCRIPTION
> # Get the probe identifiers that are mapped to gene descriptions
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+   # Get the gene descriptions for the first five probes
+   xx[1:5]
+   # For the first probe
+   xx[[1]]
+ }
[1] "Autonomously Replicating Sequence"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>