Map Open Reading Frame (ORF) Identifiers to Alias Gene Names

Description

A set of gene names may have been used to report yeast genes represented by ORF identifiers. One of these names is chosen to be the primary gene name, and the others are considered aliases. This R object provides mappings between the primary name and aliases.

Details

Each primary name maps to a vector of alias names. If there are no aliases, the vector will contain 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.sgdALIAS
# Get the probe identifiers that are mapped to alias names
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
    # Get the alias names 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.sgdALIAS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.Sc.sgdALIAS
> ### Title: Map Open Reading Frame (ORF) Identifiers to Alias Gene Names
> ### Aliases: org.Sc.sgdALIAS org.Sc.sgdALIAS2ORF
> ### 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.sgdALIAS
> # Get the probe identifiers that are mapped to alias names
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+     # Get the alias names for the first five probes
+     xx[1:5]
+     # For the first probe
+     xx[[1]]
+ }
[1] "ARSX-337"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>