CkSAApair: Composition of k-Spaced Amino Acids pairs (CkSAApair)
In ftrCOOL: Feature Extraction from Biological Sequences

Description Usage Arguments Value Note Examples

This function calculates the composition of k-spaced amino acid pairs. In other words, it computes the frequency of all amino acid pairs with k spaces.

1	CkSAApair(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 element of the vector shows the number of spaces between amino acid pairs. For each k in the rng vector, a new vector (whose size is 400) is created which contains the frequency of pairs with k gaps.
`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 [0 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).

The function returns a feature matrix. The number of rows is equal to the number of sequences and the number of columns is 400*(length of rng vector).

'upto' is enabled only when rng is a number and not a vector.

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
mat1<-CkSAApair(seqs=filePrs,rng=2,upto=TRUE,normalized=TRUE)

mat2<-CkSAApair(seqs=filePrs,rng=c(1,3,5))