Map Ensembl protein acession numbers with SGD Gene identifiers

Description

org.Sc.sgdENSEMBL is an R object that contains mappings between SGD Gene identifiers and Ensembl protein accession numbers.

Details

This object is a simple mapping of SGD Gene identifiers ftp://genome-ftp.stanford.edu/pub/yeast/data_download to Ensembl protein accession numbers.

Mappings were based on data provided by: ftp://ftp.ensembl.org/pub/current_fasta ftp://genome-ftp.stanford.edu/pub/yeast/data_download ftp://ftp.ncbi.nlm.nih.gov/gene/DATA

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.sgdENSEMBLPROT
# Get the SGD gene IDs that are mapped to an Ensembl ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the Ensembl gene IDs for the first five proteins
  xx[1:5]
  # Get the first one
  xx[[1]]
}
#For the reverse map ENSEMBLPROT2ORF:
# Convert to a list
xx <- as.list(org.Sc.sgdENSEMBLPROT2ORF)
if(length(xx) > 0){
   # Gets the SGD gene IDs for the first five Ensembl IDs
   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.sgdENSEMBLPROT.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.Sc.sgdENSEMBLPROT
> ### Title: Map Ensembl protein acession numbers with SGD Gene identifiers
> ### Aliases: org.Sc.sgdENSEMBLPROT org.Sc.sgdENSEMBLPROT2ORF
> ### 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.sgdENSEMBLPROT
> # Get the SGD gene IDs that are mapped to an Ensembl ID
> mapped_genes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_genes])
> if(length(xx) > 0) {
+   # Get the Ensembl gene IDs for the first five proteins
+   xx[1:5]
+   # Get the first one
+   xx[[1]]
+ }
[1] "Q0045"
> #For the reverse map ENSEMBLPROT2ORF:
> # Convert to a list
> xx <- as.list(org.Sc.sgdENSEMBLPROT2ORF)
> if(length(xx) > 0){
+    # Gets the SGD gene IDs for the first five Ensembl IDs
+    xx[1:5]
+    # Get the first one
+    xx[[1]]
+ }
[1] "YAL068C"   "YBL108C-A" "YGL261C"  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>