Map Between Yeast Common Names and ORF Identifiers

Description

org.Sc.sgdCOMMON2ORF is an R object that maps the yeast common names (gene names and aliases) to the corresponding yeast ORF identifiers.

Details

Each yeast common name, either gene name or alias, maps to a vector of ORF identifiers. This mapping is the reverse mappings of org.Sc.sgdGENENAME.

Mappings were based on data provided by:

Yeast Genome http://downloads.yeastgenome.org/ With a date stamp from the source of: 12-Mar-2016

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:
# Convert to a list
xx <- as.list(org.Sc.sgdCOMMON2ORF)
# Remove probes that do not map in COMMON2ORF
xx <- xx[!is.na(xx)]
if(length(xx) > 0){
    # Gets the ORF identifiers for the first five gene names/alias
    xx[1:5]
    # Get the first one
    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.sgdCOMMON2ORF.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.Sc.sgdCOMMON2ORF
> ### Title: Map Between Yeast Common Names and ORF Identifiers
> ### Aliases: org.Sc.sgdCOMMON2ORF
> ### 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:
> # Convert to a list
> xx <- as.list(org.Sc.sgdCOMMON2ORF)
> # Remove probes that do not map in COMMON2ORF
> xx <- xx[!is.na(xx)]
> if(length(xx) > 0){
+     # Gets the ORF identifiers for the first five gene names/alias
+     xx[1:5]
+     # Get the first one
+     xx[[1]]
+ }
[1] "YAL068C"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>