kNUComposition_DNA {ftrCOOL}

k Nucleotide Composition (kNUComposition_DNA)

Description

This function calculates the frequency of all k-mers in the sequence.

Usage

kNUComposition_DNA(
  seqs,
  rng = 3,
  reverse = FALSE,
  upto = FALSE,
  normalized = TRUE,
  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.

rng

This parameter can be a number or a vector. Each entry of the vector holds the value of k in the k-mer composition. For each k in the rng vector, a new vector (whose size is 4^k) is created which contains the frequency of kmers.

reverse

It is a logical parameter which assumes the reverse complement of the sequence.

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 1 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.

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 depends on the rng vector. For each value k in the vector, (4)^k columns are created in the matrix.

Examples

fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
mat<-kNUComposition_DNA(seqs=fileLNC,rng=c(1,3))