conjointTriadKS {ftrCOOL}

k-Spaced Conjoint Triad (conjointTriadKS)

Description

This function calculates the grouped tripeptide composition with conjoint triad grouping type. For each k, it creates a 7^3 feature vector. K is the space between the first and the second amino acids and the second and the third amino acids of the tripeptide.

Usage

conjointTriadKS(seqs, rng = 3, upto = FALSE, normalized = FALSE, 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 the first and the second amino acids and the second and the third amino acids of the tripeptide. For each k in the rng vector, a new vector (whose size is 7^3) is created which contains the frequency of tri-amino acid 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).

Details

A tripeptide with k spaces looks like AA1(ss..s)AA2(ss..s)AA3. AA stands for amino acids and s means space.

Value

This function returns a feature matrix. The number of rows is equal to the number of sequences and the number of columns is (7^3)*(length 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<-conjointTriadKS(filePrs,rng=2,upto=TRUE,normalized=TRUE)

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