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#' Z_curve_144bit_DNA (Zcurve144bit_DNA)
#'
#' 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.
#'
#' @references Gao,F. and Zhang,C.T. Comparison of various algorithms for recognizing short coding sequences of human genes. Bioinformatics, (2004).
#'
#' @param 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.
#'
#' @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 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 is equal to the number of sequences and
#' the number of columns is 144.
#'
#' @export
#'
#' @examples
#'
#' fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
#' mat<-Zcurve144bit_DNA(seqs=fileLNC,ORF=TRUE,reverseORF=FALSE)
Zcurve144bit_DNA<-function(seqs,ORF=FALSE,reverseORF=TRUE,label=c()){
if(length(seqs)==1&&file.exists(seqs)){
seqs<-fa.read(seqs,alphabet="dna")
seqs_Lab<-alphabetCheck(seqs,alphabet = "dna",label)
seqs<-seqs_Lab[[1]]
label<-seqs_Lab[[2]]
}
else if(is.vector(seqs)){
seqs<-sapply(seqs,toupper)
seqs_Lab<-alphabetCheck(seqs,alphabet = "dna",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(seqs,reverse=reverseORF)
if(flag==1)
label=label[names(seqs)]
}
numSeqs<-length(seqs)
lenSeqs<-sapply(seqs,nchar)
er<-which(lenSeqs<5)
if(length(er)!=0){
stop(paste("Sequnse/Sequnses",er,"is/are smaller than minSize(5)"))
}
DiNuc<-nameKmer(k=2,type = "dna")
TriNuc<-nameKmer(k=3,type = "dna")
featureMatrix<-matrix(ncol = 144,nrow = numSeqs)
for(n in 1:numSeqs){
seq<-seqs[n]
lenSeq<-lenSeqs[n]
PosInd1<-seq(1,lenSeq,3)
PosInd1<-PosInd1[(PosInd1+2)<=lenSeq]
EndPos1<-PosInd1+2
PosInd2<-seq(2,lenSeq,3)
PosInd2<-PosInd2[(PosInd2+2)<=lenSeq]
EndPos2<-PosInd2+2
PosInd3<-seq(3,lenSeq,3)
PosInd3<-PosInd3[(PosInd3+2)<=lenSeq]
EndPos3<-PosInd3+2
TrimPos1<-substring(seq,PosInd1,EndPos1)
TrimPos2<-substring(seq,PosInd2,EndPos2)
TrimPos3<-substring(seq,PosInd3,EndPos3)
freqTrimPos1<-rep(0,64)
names(freqTrimPos1)<-TriNuc
freqTrimPos2<-rep(0,64)
names(freqTrimPos2)<-TriNuc
freqTrimPos3<-rep(0,64)
names(freqTrimPos3)<-TriNuc
TrimPos1<-table(TrimPos1)
TrimPos2<-table(TrimPos2)
TrimPos3<-table(TrimPos3)
freqTrimPos1[names(TrimPos1)]<-TrimPos1
freqTrimPos2[names(TrimPos2)]<-TrimPos2
freqTrimPos3[names(TrimPos3)]<-TrimPos3
Pxa=freqTrimPos1[paste(DiNuc,"A",sep="")]
Pxg=freqTrimPos1[paste(DiNuc,"G",sep="")]
Pxc=freqTrimPos1[paste(DiNuc,"C",sep="")]
Pxt=freqTrimPos1[paste(DiNuc,"T",sep="")]
xVect1<-(Pxa+Pxg)-(Pxc+Pxt)
yVect1<-(Pxa+Pxc)-(Pxg+Pxt)
zVect1<-(Pxa+Pxt)-(Pxg+Pxc)
Pxa2=freqTrimPos2[paste(DiNuc,"A",sep="")]
Pxg2=freqTrimPos2[paste(DiNuc,"G",sep="")]
Pxc2=freqTrimPos2[paste(DiNuc,"C",sep="")]
Pxt2=freqTrimPos2[paste(DiNuc,"T",sep="")]
xVect2<-(Pxa2+Pxg2)-(Pxc2+Pxt2)
yVect2<-(Pxa2+Pxc2)-(Pxg2+Pxt2)
zVect2<-(Pxa2+Pxt2)-(Pxg2+Pxc2)
Pxa3=freqTrimPos3[paste(DiNuc,"A",sep="")]
Pxg3=freqTrimPos3[paste(DiNuc,"G",sep="")]
Pxc3=freqTrimPos3[paste(DiNuc,"C",sep="")]
Pxt3=freqTrimPos3[paste(DiNuc,"T",sep="")]
xVect3<-(Pxa3+Pxg3)-(Pxc3+Pxt3)
yVect3<-(Pxa3+Pxc3)-(Pxg3+Pxt3)
zVect3<-(Pxa3+Pxt3)-(Pxg+Pxc3)
mat<-rbind(xVect1,yVect1,zVect1,xVect2,yVect2,zVect2,xVect3,yVect3,zVect3)
featureMatrix[n,]<-as.vector(mat)/(lenSeq-2)
}
tempName1<-rep(DiNuc,each=9)
tempName2<-rep(c("x","y","z"),48)
tempName3<-rep(c("1","2","3"),each=3)
tmp<-paste0("Pos.",tempName3,".",tempName1,".",tempName2)
colnames(featureMatrix)<-tmp
if(length(label)==numSeqs){
featureMatrix<-as.data.frame(featureMatrix)
featureMatrix<-cbind(featureMatrix,label)
}
return(featureMatrix)
}
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