CkSAApair {ftrCOOL}

Composition of k-Spaced Amino Acids pairs (CkSAApair)

Description

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.

Usage

CkSAApair(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 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).

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*(length of rng vector).

Note

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

Examples

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))