Picks a prioritised RefSeq identifier from a list of identifiers
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Vector or list of RefSeqs accessions to pick from. If list given, applies the prioritation to each element in the list.
Character vector of prioritised prefixes to pick by. Eg.
Reducing method, either return all annotations (one-to-many relation)
or the first or last found annotation. The reducing step is applied
after translating to the goal:
When translating to RefSeq, typically multiple identifiers are returned,
referring to different types of products, such as genomic molecule, mature
mRNA or the protein, and they can be predicted, properties that can be read
from the prefix (http://www.ncbi.nlm.nih.gov/refseq/key.html). E.g. "XM_" is
predicted mRNA and "NP_" is a protein. Run
If vector given, returns vector. If list given, returns list without element where nothing could be picked.
Stefan McKinnon Edwards [email protected]
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library(org.Bt.eg.db) symbols <- c("SERPINA1","KERA","CD5") refseq <- translate(symbols, from=org.Bt.egSYMBOL2EG, to=org.Bt.egREFSEQ) mRNA <- pickRefSeq(refseq, priorities=c('NM','XM')) proteins <- pickRefSeq(refseq, priorities=c('NP','XP')) # The same. mRNA <- pickRefSeq.mRNA(refseq) proteins <- pickRefSeq.Protein(refseq)
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