SOCNumber {ftrCOOL}

Sequence Order Coupling Number (SOCNumber)

Description

This function uses dissimilarity matrices Grantham and Schneider to compute the dissimilarity between amino acid pairs. The distance between amino acid pairs is determined by d which varies between 1 to nlag. For each d, it computes the sum of the dissimilarities of all amino acid pairs. The sum shows the value of tau for a value d. The feature vector contains the values of taus for both matrices. Thus, the length of the feature vector is equal to nlag*2.

Usage

SOCNumber(seqs, nlag = 30, label = c())

Arguments

seqs

is a FASTA file with amino acid sequences. Each sequence starts with a '>' character. Also, seqs could be a string vector. Each element of the vector is a peptide/protein sequence.

nlag

is a numeric value which shows the maximum distance between two amino acids. Distances can be 1, 2, ..., or nlag. Defult is 30.

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

It returns a feature matrix. The number of rows is equal to the number of sequences and the number of columns is (nlag*2). For each distance d, there are two values. One value for Granthman and another one for Schneider distance.

Note

When d=1, the pairs of amino acids have no gap and when d=2, there is one gap between the amino acid pairs in the sequence. It will repeat likewise for other values of d.

Examples

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")

mat<-SOCNumber(seqs=filePrs,nlag=25)