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#' Expected Value for K-mer Amino Acid (ExpectedValueKmerAA)
#'
#' This function computes the expected value of each k-mer by dividing the frequency of the
#' kmer to multiplying frequency of each amino acid of the k-mer in the sequence.
#'
#' ExpectedValue(k-mer) = freq(k-mer) / ( freq(aminoacid1) * freq(aminoacid2) * ... * freq(aminoacidk) )
#'
#' @param 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.
#'
#' @param k is an integer value and it shows the size of kmer in the kmer composition. The default value is 2.
#'
#' @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 This function returns a feature matrix. The number of rows equals the number of sequences and
#' the number of columns if upto set false, is 20^k.
#'
#'
#' @export
#'
#' @examples
#'
#' filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
#' mat<-ExpectedValueKmerAA(filePrs,k=2,normalized=FALSE)
ExpectedValueKmerAA<-function(seqs,k=2,normalized=TRUE,label=c())
{
if(length(seqs)==1&&file.exists(seqs)){
seqs<-fa.read(seqs,alphabet="aa")
seqs_Lab<-alphabetCheck(seqs,alphabet = "aa",label)
seqs<-seqs_Lab[[1]]
label<-seqs_Lab[[2]]
}
else if(is.vector(seqs)){
seqs<-sapply(seqs,toupper)
seqs_Lab<-alphabetCheck(seqs,alphabet = "aa",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.")
}
numSeqs<-length(seqs)
featureMatrix<-kAAComposition(seqs,rng=k,normalized =FALSE)
AAcompos<-kAAComposition(seqs,rng=1,normalized =FALSE)
for(i in 1:ncol(featureMatrix)){
chars<-unlist(strsplit(colnames(featureMatrix)[i],split = ""))
composMat<-AAcompos[,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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