kAAComposition {ftrCOOL}

k Amino Acid Composition (kAAComposition)

Description

This function calculates the frequency of all k-mers in the sequence(s).

Usage

kAAComposition(seqs, rng = 3, upto = FALSE, 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.

rng

This parameter can be a number or a vector. Each entry of the vector holds the value of k in the k-mer composition.

upto

It is a logical parameter. The default value is FALSE. If rng is a number and upto is set to TRUE, rng is converted to a vector with values from 1 to rng.

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

This function returns a feature matrix. The number of rows is equal to the number of sequences and the number of columns depends on rng vector. For each value k in the vector, (20)^k columns are created in the matrix.

Examples

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

mat1<-kAAComposition(seqs=filePrs,rng=3,upto=TRUE)
mat2<-kAAComposition(seqs=filePrs,rng=c(1,3),upto=TRUE)