maxORFlength_DNA {ftrCOOL}

Maximum Open Reading Frame length in DNA (maxORFlength_DNA)

Description

This function returns the length of the maximum Open Reading Frame for each sequence. If reverse is FALSE, ORF region will be searched in a sequence. Otherwise, it will be searched both in the sequence and its reverse complement.

Usage

maxORFlength_DNA(seqs, reverse = TRUE, normalized = FALSE, label = c())

Arguments

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.

normalized

is a logical parameter. When it is FALSE, the return value of the function does not change. Otherwise, the return value is normalized using the length 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).

Value

A vector containing the lengths of maximum ORFs for each sequence.

Examples

fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
vect<-maxORFlength_DNA(seqs=fileLNC,reverse=TRUE,normalized=TRUE)