Description Usage Arguments Value Note Examples
This function gets a sequence as the input. If reverse is true, the function extracts the max Open Reading Frame in the sequence and its reverse complement (hint: Six frames). Otherwise, only the sequence is searched (hint: Three frames).
1 |
seqs |
is a FASTA file containing nucleotide sequences. The sequences start with '>'. Also, seqs could be a string vector. Each element of the vector is a nucleotide sequence. |
reverse |
It is a logical parameter which assumes the reverse complement of the sequence. |
label |
is an optional parameter. It is a vector whose length is equivalent to the number of sequences. It shows the class of each entry (i.e., sequence). |
A vector containing a subsequence for each given sequences. The subsequence is the maximum ORF of the sequence.
If a sequence does not contain ORF, the function deletes the sequence.
1 2 | fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
ORF<-maxORF(seqs=fileLNC,reverse=FALSE)
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