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#' Z_curve_36bit_RNA (Zcurve36bit_RNA)
#'
#' These group of functions (Zcurve (9, 12, 36, 48, 144)_bit) function calculates the Z-curves. Z-curves are based on freqiencies of ribonucleotides, di-ribonucleotides, or tri-ribonucleotides 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 ribonucleotide sequences. The sequences start
#' with '>'. Also, seqs could be a string vector. Each element of the vector is a ribonucleotide 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 36.
#'
#' @export
#'
#' @examples
#'
#' fileLNC<-system.file("extdata/Carica_papaya101RNA.txt",package="ftrCOOL")
#' mat<-Zcurve36bit_RNA(seqs=fileLNC,ORF=TRUE,reverseORF=FALSE)
Zcurve36bit_RNA<-function(seqs,ORF=FALSE,reverseORF=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)
lenSeqs<-sapply(seqs,nchar)
DiNuc<-nameKmer(k=2,type = "rna")
featureMatrix<-matrix(ncol = 36,nrow = numSeqs)
for(n in 1:numSeqs){
seq<-seqs[n]
lenSeq<-lenSeqs[n]
PosInd1<-seq(1,lenSeq,3)
PosInd1<-PosInd1[(PosInd1+1)<=lenSeq]
EndPos1<-PosInd1+1
PosInd2<-seq(2,lenSeq,3)
PosInd2<-PosInd2[(PosInd2+1)<=lenSeq]
EndPos2<-PosInd2+1
PosInd3<-seq(3,lenSeq,3)
PosInd3<-PosInd3[(PosInd3+1)<=lenSeq]
EndPos3<-PosInd3+1
DimPos1<-substring(seq,PosInd1,EndPos1)
DimPos2<-substring(seq,PosInd2,EndPos2)
DimPos3<-substring(seq,PosInd3,EndPos3)
freqDimPos1<-rep(0,16)
names(freqDimPos1)<-DiNuc
freqDimPos2<-rep(0,16)
names(freqDimPos2)<-DiNuc
freqDimPos3<-rep(0,16)
names(freqDimPos3)<-DiNuc
DimPos1<-table(DimPos1)
DimPos2<-table(DimPos2)
DimPos3<-table(DimPos3)
freqDimPos1[names(DimPos1)]<-DimPos1
freqDimPos2[names(DimPos2)]<-DimPos2
freqDimPos3[names(DimPos3)]<-DimPos3
Nucs<-c("A","C","G","U")
mat1<-matrix(nrow = 3,ncol = 4)
rownames(mat1)<-c("x","y","z")
colnames(mat1)<-c("A","C","G","U")
for(i in 1:4){
Pxa=freqDimPos1[paste(Nucs[i],"A",sep="")]
Pxg=freqDimPos1[paste(Nucs[i],"G",sep="")]
Pxc=freqDimPos1[paste(Nucs[i],"C",sep="")]
Pxt=freqDimPos1[paste(Nucs[i],"U",sep="")]
mat1["x",i]<-(Pxa+Pxg)-(Pxc+Pxt)
mat1["y",i]<-(Pxa+Pxc)-(Pxg+Pxt)
mat1["z",i]<-(Pxa+Pxt)-(Pxg+Pxc)
}
mat2<-matrix(nrow = 3,ncol = 4)
rownames(mat2)<-c("x","y","z")
colnames(mat2)<-c("A","C","G","U")
for(i in 1:4){
Pxa=freqDimPos2[paste(Nucs[i],"A",sep="")]
Pxg=freqDimPos2[paste(Nucs[i],"G",sep="")]
Pxc=freqDimPos2[paste(Nucs[i],"C",sep="")]
Pxt=freqDimPos2[paste(Nucs[i],"U",sep="")]
mat2["x",i]<-(Pxa+Pxg)-(Pxc+Pxt)
mat2["y",i]<-(Pxa+Pxc)-(Pxg+Pxt)
mat2["z",i]<-(Pxa+Pxt)-(Pxg+Pxc)
}
mat3<-matrix(nrow = 3,ncol = 4)
rownames(mat3)<-c("x","y","z")
colnames(mat3)<-c("A","C","G","U")
for(i in 1:4){
Pxa=freqDimPos3[paste(Nucs[i],"A",sep="")]
Pxg=freqDimPos3[paste(Nucs[i],"G",sep="")]
Pxc=freqDimPos3[paste(Nucs[i],"C",sep="")]
Pxt=freqDimPos3[paste(Nucs[i],"U",sep="")]
mat3["x",i]<-(Pxa+Pxg)-(Pxc+Pxt)
mat3["y",i]<-(Pxa+Pxc)-(Pxg+Pxt)
mat3["z",i]<-(Pxa+Pxt)-(Pxg+Pxc)
}
mat<-rbind(mat1,mat2,mat3)
featureMatrix[n,]<-as.vector(mat)/(lenSeq-1)
}
tempName1<-rep(c("A","C","G","U"),each=9)
tempName2<-rep(c("x","y","z"),12)
temp3<-rep(c("1","2","3"),each=3)
colnames(featureMatrix)<-paste0("Pos.",temp3,".",tempName1,".",tempName2)
if(length(label)==numSeqs){
featureMatrix<-as.data.frame(featureMatrix)
featureMatrix<-cbind(featureMatrix,label)
}
return(featureMatrix)
}
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