org.At.tairREFSEQ {org.At.tair.db} | R Documentation |
org.At.tairREFSEQ is an R object that provides mappings between TAIR identifiers and RefSeq identifiers.
Each TAIR identifier is mapped to a named vector of RefSeq
identifiers. The name represents the TAIR identifier and the vector
contains all RefSeq identifiers that can be mapped to that TAIR
identifier. The length of the vector may be one or greater, depending
on how many RefSeq identifiers a given TAIR identifier can be mapped
to. An NA
is reported for any TAIR 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: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/RefSeq/
x <- org.At.tairREFSEQ # Get the TAIR 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.At.tairREFSEQ2TAIR # Get the RefSeq identifier that are mapped to an TAIR ID mapped_seqs <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_seqs]) if(length(xx) > 0) { # Get the TAIR ID for the first five Refseqs xx[1:5] # Get the first one xx[[1]] }