alphabetCheck {ftrCOOL}

AlphabetCheck

Description

This function checks the alphabets in a sequence. If one of the following conditions hold, the sequence will be deleted: 1. A peptide sequence containing non-standard amino acids, 2. A DNA sequence with an alphabet other than A, C, G, or T, 3. An RNA sequence having an alphabet other than A, C, G, or U.

Usage

alphabetCheck(sequences, alphabet = "aa", label = c())

Arguments

sequences

is a string vector. Each element is a peptide, protein, DNA, or RNA sequences.

alphabet

This parameter shows the alphabet of sequences. If it is set to 'aa', it indicates the alphabet of amino acids. When it is 'dna', it shows the nucleotide alphabet and in case it equals 'rna', it represents ribonucleotide alphabet.

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

'alphabetCheck' returns a list with two elements. The first element is a vector which contains valid sequences. The second element is a vector which contains the labels of the sequences (if any exists).

Note

This function receives a sequence vector and the label of sequences (if any). It deletes sequences (and their labels) containing non-standard alphabets.

Examples

seq<-alphabetCheck(sequences=c("AGDFLIAACNMLKIVYT","ADXVGAJK"),alphabet="aa")