hgu95av2REFSEQ {hgu95av2}R Documentation

Map between Manufacturer Identifiers and RefSeq Identifiers

Description

hgu95av2REFSEQ is an R environment that provides mappings between manufacturer ids and RefSeq ids.

Details

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

RefSeq ids differ in format according to the type of record the ids 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 ids.

Mappings were based on data provided by:

Entrez Gene:http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Tue Oct 4 21:15:59 2005

Package built Tue Oct 4 21:31:35 2005

References

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

Examples

    # Convert the environment to a list
    xx <- as.list(hgu95av2REFSEQ)
    # Remove probe ids that do not map to any RefSeq
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
    # The RefSeq for the first two elements of XX
    xx[1:2]
    # Get the first one
    xx[[1]]
}

[Package hgu95av2 version 1.10.0 Index]