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

Map between systematic ORF identifiers and RefSeq Identifiers

Description

org.Sc.sgdREFSEQ is an R object that provides mappings between systematic ORF identifiers and RefSeq identifiers.

Details

Each systematic ORF identifier is mapped to a named vector of RefSeq identifiers. The name represents the systematic ORF identifier and the vector contains all RefSeq identifiers that can be mapped to that entrez gene identifier. The length of the vector may be one or greater, depending on how many RefSeq identifiers a given systematic ORF identifier can be mapped to. An NA is reported for any entrex gene identifier that cannot be mapped to a RefSeq identifier at this time.

RefSeq identifiers differ in format according to the type of record the identifiers are for as shown below:

NG\_XXXXX: RefSeq accessions for genomic region (nucleotide) records

NM\_XXXXX: RefSeq accessions for mRNA records

NC\_XXXXX: RefSeq accessions for chromosome records

NP\_XXXXX: RefSeq accessions for protein records

XR\_XXXXX: RefSeq accessions for model RNAs that are not associated with protein products

XM\_XXXXX: RefSeq accessions for model mRNA records

XP\_XXXXX: RefSeq accessions for model protein records

Where XXXXX is a sequence of integers.

NCBI http://www.ncbi.nlm.nih.gov/RefSeq/ allows users to query the RefSeq database using RefSeq identifiers.

Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA With a date stamp from the source of: 2011-Sep14

References

http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/RefSeq/

Examples

        x <- org.Sc.sgdREFSEQ
        # Get the systematic ORF identifiers that are mapped to any RefSeq ID
        mapped_genes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_genes])
        if(length(xx) > 0) {
          # Get the REFSEQ for the first five genes
          xx[1:5]
          # Get the first one
          xx[[1]]
        }


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