ASDC: Adaptive skip dipeptide composition (ASDC)

In ftrCOOL: Feature Extraction from Biological Sequences

Description

This descriptor sufficiently considers the correlation information present not only between adjacent residues but also between intervening residues. This function calculates frequency of pair amino acids omitting gaps between them. Then this function normalizes each value through dividing each frequency by summition(frequencies).

Usage

ASDC(seqs, 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.
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

The function returns a feature matrix. The number of rows is equal to the number of sequences and the number of columns is 400 (all posible amino acid pairs).

References

Wei L, Zhou C, Chen H, Song J, Su R. ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides. Bioinformatics (2018).

Examples

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

ftrCOOL documentation built on Nov. 30, 2021, 1:07 a.m.