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

Examples

    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]]
    }