org.Hs.egREFSEQ {org.Hs.eg.db} | R Documentation |
org.Hs.egREFSEQ is an R object that provides mappings between entrez gene identifiers and RefSeq identifiers.
Each entrez gene identifier is mapped to a named vector of RefSeq
identifiers. The name represents the entrez gene 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 entrez gene
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 ) on 2008-Apr2
http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/RefSeq/
x <- org.Hs.egREFSEQ # Get the entrez gene 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]] } # For the reverse map: x <- org.Hs.egREFSEQ2EG # Get the RefSeq identifier that are mapped to an entrez gene ID mapped_seqs <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_seqs]) if(length(xx) > 0) { # Get the entrez gene for the first five Refseqs xx[1:5] # Get the first one xx[[1]] }