conjointTriad {ftrCOOL}

Conjoint Triad (conjointTriad)

Description

This function calculates the grouped tripeptide composition with the conjoint triad grouping type.

Usage

conjointTriad(seqs, 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.

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 equals to the number of sequences and the number of columns is 7^3.

Examples

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
mat1<-conjointTriad(seqs=filePrs)