Map Ensembl gene accession numbers with SGD Gene identifiers

Description

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

Details

This object is a simple mapping of SGD Gene identifiers ftp://genome-ftp.stanford.edu/pub/yeast/data_download to Ensembl gene Accession Numbers.

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

This mapping is a combination of NCBI to ensembl IDs from BOTH NCBI and ensembl. These mappings are based upon the ensembl table which is contains data from BOTH of these sources in an effort to maximize the chances that you will find a match.

Mappings were based on data provided by: Ensembl ftp://ftp.ensembl.org/pub/current_fasta With a date stamp from the source of: 2016-Mar9

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.sgdENSEMBL
# 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 genes
  xx[1:5]
  # Get the first one
  xx[[1]]
}
#For the reverse map ENSEMBL2ORF:
# Convert to a list
xx <- as.list(org.Sc.sgdENSEMBL2ORF)
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.sgdENSEMBL.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.Sc.sgdENSEMBL
> ### Title: Map Ensembl gene accession numbers with SGD Gene identifiers
> ### Aliases: org.Sc.sgdENSEMBL org.Sc.sgdENSEMBL2ORF
> ### 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.sgdENSEMBL
> # 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 genes
+   xx[1:5]
+   # Get the first one
+   xx[[1]]
+ }
[1] "Q0045"
> #For the reverse map ENSEMBL2ORF:
> # Convert to a list
> xx <- as.list(org.Sc.sgdENSEMBL2ORF)
> 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 
>