ftrCOOL (version 2.0.0)

CkSNUCpair_DNA: Composition of k-Spaced Nucleotides Pairs (CkSNUCpair_DNA)

Description

This function calculates the composition of k-spaced nucleotide pairs. In other words, it computes the frequency of all nucleotide pairs with k spaces.

Usage

CkSNUCpair_DNA(
  seqs,
  rng = 3,
  upto = FALSE,
  ORF = FALSE,
  reverseORF = TRUE,
  normalized = 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 element of the vector shows the number of spaces between nucleotide pairs. For each k in the rng vector, a new vector (whose size is 16) is created which contains the frequency of pairs with k gaps.

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 [0 to rng].

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).

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

The function returns a feature matrix. The number of rows is equal to the number of sequences and the number of columns is 16*(length of rng vector).

Examples

# NOT RUN {

fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
mat1<-CkSNUCpair_DNA(seqs=fileLNC,rng=2,upto=TRUE,ORF=TRUE,reverseORF=FALSE)
mat2<-CkSNUCpair_DNA(seqs=fileLNC,rng=c(1,3,5))

# }