zebrafishREFSEQ {zebrafish.db} | R Documentation

## Map between Manufacturer Identifiers and RefSeq Identifiers

### Description

zebrafishREFSEQ is an R object that provides mappings between manufacturer identifiers and RefSeq identifiers.

### Details

Each manufacturer identifier is mapped to a named vector of RefSeq identifiers. The name represents the manufacturer identifier and the vector contains all RefSeq identifiers that can be mapped to that manufacturer identifier. The length of the vector may be one or greater, depending on how many RefSeq identifiers a given manufacturer identifier can be mapped to. An `NA` is reported for any manufacturer 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 ) on 2009-Mar11

### References

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

### Examples

            x <- zebrafishREFSEQ
            # Get the probe identifiers that are mapped to any RefSeq ID
            mapped_probes <- mappedkeys(x)
            # Convert to a list
            xx <- as.list(x[mapped_probes])
            if(length(xx) > 0) {
              # Get the REFSEQ for the first five probes
              xx[1:5]
              # Get the first one
              xx[[1]]
            }

[Package zebrafish.db version 2.2.11 Index]