org.Sc.sgdENSEMBL {org.Sc.sgd.db}R Documentation

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: 2011-Jun30

Examples

    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]]
    }

[Package org.Sc.sgd.db version 2.6.4 Index]