org.Sc.sgdREFSEQ {org.Sc.sgd.db} | R Documentation |
org.Sc.sgdREFSEQ is an R object that provides mappings between systematic ORF identifiers and RefSeq identifiers.
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
http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/RefSeq/
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]] }