Zcurve9bit_DNA {ftrCOOL}

Z_curve_9bit_DNA (Zcurve9bit_DNA)

Description

These group of functions (Zcurve (9, 12, 36, 48, 144)_bit) function calculates the Z-curves. Z-curves are based on freqiencies of nucleotides, di-nucleotides, or tri-nucleotides and their positions on the sequences. For more information about the methods please refer to reference part.

Usage

Zcurve9bit_DNA(seqs, ORF = FALSE, reverseORF = TRUE, label = c())

Arguments

seqs

is a FASTA file containing nucleotide sequences. The sequences start with '>'. Also, seqs could be a string vector. Each element of the vector is a nucleotide sequence.

ORF

(Open Reading Frame) is a logical parameter. If it is set to true, ORF region of each sequence is considered instead of the original sequence (i.e., 3-frame).

reverseORF

is a logical parameter. It is enabled only if ORF is true. If reverseORF is true, ORF region will be searched in the sequence and also in the reverse complement of the sequence (i.e., 6-frame).

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 9.

References

Gao,F. and Zhang,C.T. Comparison of various algorithms for recognizing short coding sequences of human genes. Bioinformatics, (2004).

Examples

fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
mat<-Zcurve9bit_DNA(seqs=fileLNC,ORF=TRUE,reverseORF=FALSE)