findORFs {ORFik} | R Documentation |
Find all Open Reading Frames (ORFs) on the input sequences
in 5'- 3' direction, but within all three possible reading frames. For each
sequence of the input vector IRanges
with START and
STOP positions (inclusive) will be returned as
IRangesList
. Returned coordinates are relative to the
input sequences.
findORFs(seqs, startCodon = startDefinition(1), stopCodon = stopDefinition(1), longestORF = FALSE, minimumLength = 0)
seqs |
(DNAStringSet or character) DNA sequences to search for Open Reading Frames. |
startCodon |
(character) Possible START codons to search for. Check [startDefinition()] for helper function. |
stopCodon |
(character) Possible STOP codons to search for. Check [stopDefinition()] for helper function. |
longestORF |
(logical) Default FALSE. When TRUE will only report ORFs that are longest, all smaller overlapping ORFs will be ignored. When FALSE will report all possible ORFs in all three reading frames. |
minimumLength |
(integer) Default is 0. Minimum length of ORF, without counting 3bp for START and STOP codons. For example minimumLength = 8 will result in size of ORFs to be at least START + 8*3 (bp) + STOP. Use this param to restrict search. |
(IRangesList) of ORFs locations incuding START and STOP codons grouped by input seqeunces.
[findMapORFs()], [findORFsFasta()], [startDefinition()], [stopDefinition()]
Other findORFs: findMapORFs
,
findORFsFasta
,
startDefinition
,
stopDefinition
findORFs("ATGTAA") findORFs("ATGTTAA") # not in frame anymore findORFs("ATGATGTAA") # two ORFs findORFs("ATGATGTAA", longestORF = TRUE) # only longest of two above findORFs(c("ATGTAA", "ATGATGTAA"))