getOrfs {GeneR} | R Documentation |
Gets ORFs (Open Reading Frames) from a sequence.
getOrfs(phase = NULL,seqno=0,start="atg", stop=c("taa","tag","tga"), complete = TRUE,suborfs=TRUE) maxOrf(seqno=0,phase = NULL,start="atg", stop=c("taa","tag","tga"), complete = TRUE)
seqno |
Integer/scalar, Sequence number (buffer number) |
phase |
Integer/scalar,. 1,2 or 3, NULL for all three phases |
start |
string/vector, start codons |
stop |
string/vector, stop codons |
complete |
Flag: true returns only complet Orfs, else return all Orfs. |
suborfs |
Flag: true returns all orfs including subparts of a large orf if it exists "atg" in the phase. False: does not returns sub-orfs. |
getOrf returns a table of positions. NULL if no Orfs.
maxOrf returns the size of the largest Orf, -1 if no Orf.
All functions return NA if error.
Reverse strand : not implemented
A. Lucas, Emna Marrakchi and Vincent Lefort
s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa" placeString(s) getOrfs(phase = NULL,seqno=0) maxOrf() # To get all ORFs on the reverse strand: sc <- getSeq(0,1) placeString(sc,seqno=1) getOrfs(phase = NULL,seqno=1) # All orfs on both strands : rbind(getOrfs(seqno=0),getOrfs(seqno=1))