AAKpartComposition: Amino Acid to K Part Composition (AAKpartComposition)

In ftrCOOL: Feature Extraction from Biological Sequences

Description

In this function, each sequence is divided into k equal partitions. The length of each part is equal to ceiling(l(lenght of the sequence)/k). The last part can have a different length containing the residual amino acids. The amino acid composition is calculated for each part.

Usage

AAKpartComposition(seqs, k = 3, normalized = TRUE, 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.
k	is an integer value. Each sequence should be divided to k partition(s).
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 feature matrix with k*20 number of columns. The number of rows is equal to the number of sequences.

Note

Warning: The length of all sequences should be greater than k.

Examples

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
mat<-AAKpartComposition(seqs=filePrs,k=5,normalized=FALSE)

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