kAAComposition: k Amino Acid Composition (kAAComposition)
In ftrCOOL: Feature Extraction from Biological Sequences

Description Usage Arguments Value Examples

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

1	kAAComposition(seqs, rng = 3, upto = FALSE, normalized = TRUE, label = c())

`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).

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.

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)