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#' Expected Value for K-mer riboNucleotide (ExpectedValKmerNUC_RNA)
#'
#' This function is introduced by this package for the first time.
#' It computes the expected value for each k-mer in a sequence.
#' ExpectedValue(k-mer) = freq(k-mer) / ( freq(ribonucleotide1) * freq(ribonucleotide2) * ... * freq(ribonucleotidek) )
#'
#' @param seqs is a FASTA file containing ribonucleotide sequences. The sequences start
#' with '>'. Also, seqs could be a string vector. Each element of the vector is a ribonucleotide sequence.
#'
#' @param k is an integer value. The default is four.
#'
#' @param 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).
#'
#' @param 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).
#'
#' @param 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.
#'
#' @param 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).
#'
#' @return The function returns a feature matrix. The number of rows is equal to the number of sequences and
#' the number of columns is (4^k).
#'
#'
#' @export
#'
#' @examples
#'
#' fileLNC<-system.file("extdata/Carica_papaya101RNA.txt",package="ftrCOOL")
#' mat<-ExpectedValKmerNUC_RNA(seqs=fileLNC,k=4,ORF=TRUE,reverseORF=FALSE)
ExpectedValKmerNUC_RNA<-function(seqs,k=4,ORF=FALSE,reverseORF=TRUE,normalized=TRUE,label=c())
{
if(length(seqs)==1&&file.exists(seqs)){
seqs<-fa.read(seqs,alphabet="rna")
seqs_Lab<-alphabetCheck(seqs,alphabet = "rna",label)
seqs<-seqs_Lab[[1]]
label<-seqs_Lab[[2]]
}
else if(is.vector(seqs)){
seqs<-sapply(seqs,toupper)
seqs_Lab<-alphabetCheck(seqs,alphabet = "rna",label)
seqs<-seqs_Lab[[1]]
label<-seqs_Lab[[2]]
}
else {
stop("ERROR: Input sequence is not in the correct format. It should be a FASTA file or a string vector.")
}
flag=0
if(ORF==TRUE){
if(length(label)==length(seqs)){
names(label)=names(seqs)
flag=1
}
seqs=maxORF_RNA(seqs,reverse=reverseORF)
if(flag==1)
label=label[names(seqs)]
}
numSeqs<-length(seqs)
featureMatrix<-kNUComposition_RNA(seqs,reverse=FALSE,rng=k,normalized=FALSE)
NUCompos<-kNUComposition_RNA(seqs,rng=1,reverse=FALSE,normalized=FALSE)
for(i in 1:ncol(featureMatrix)){
chars<-unlist(strsplit(colnames(featureMatrix)[i],split = ""))
composMat<-NUCompos[,chars]
if(is.matrix(composMat)){
mult<-apply(composMat, 1, prod)
} else {
mult<-prod(composMat)
}
featureMatrix[,i]<-featureMatrix[,i]/mult
}
featureMatrix[is.na(featureMatrix)]=0
featureMatrix[is.infinite(featureMatrix)]=0
if(normalized==TRUE){
seqLen<-sapply(seqs, nchar)
featureMatrix<-featureMatrix/seqLen
}
if(length(label)==numSeqs){
featureMatrix<-as.data.frame(featureMatrix)
featureMatrix<-cbind(featureMatrix,label)
}
row.names(featureMatrix)<-names(seqs)
return(featureMatrix)
}
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