CTD {ftrCOOL}

Composition_Transition_Distribution (CTD)

Description

This function calculates the composition, transition, and distribution for each sequence.

Usage

CTD(seqs, 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.

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

Output is a combination of three different matrices: Composition, Transition, and Distribution. You can obtain any of the three matrices by executing the corresponding function, i.e., CTDC, CTDT, and CTDD.

References

Dubchak, Inna, et al. "Prediction of protein folding class using global description of amino acid sequence." Proceedings of the National Academy of Sciences 92.19 (1995): 8700-8704.

Examples

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
CTDtotal<-CTD(seqs=filePrs,normalized=FALSE)