CTDC {ftrCOOL}

CTD Composition (CTDC)

Description

This function computes the composition part of CTD. Thirteen properties are defined in this function. Each property categorizes the amino acids of the sequences into three groups. The grouped amino acid composition is calculated for each property. For more information, please check the references.

Usage

CTDC(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

This function returns a feature matrix. The number of rows is equal to the number of sequences and the number of columns is 3*7, where three is the number of groups and thirteen is the number of properties.

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")
CTD_C<-CTDC(seqs=filePrs,normalized=FALSE,label=c())