R/DiNUCindex_RNA.R

In ftrCOOL: Feature Extraction from Biological Sequences

#' Di riboNucleotide Index (DiNUCindex_RNA)
#'
#' This function replaces di-ribonucleotides in a sequence with their physicochemical properties in the di-ribonucleotide index file.
#'
#'
#' @details There are 22 physicochemical indexes in the di-ribonucleotide database.
#'
#' @note This function is provided for sequences with the same lengths.
#' Users can use 'txt' option in outFormat for sequences with different lengths.
#' Warning: If outFormat is set to 'mat' for sequences with different lengths, it returns an error.
#' Also, when output format is 'txt', label information is not shown in the text file.
#' It is noteworthy that 'txt' format is not usable for machine learning purposes if sequences have different sizes. Otherwise 'txt' format
#' is also usable for machine learning purposes.
#'
#' @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 selectedIdx DiNucIndex function works based on physicochemical properties. Users, select the properties by their ids
#' or indexes in DI_RNA file.
#' The default value of this parameter is a vector with ("Rise (RNA)", "Roll (RNA)", "Shift (RNA)", "Slide (RNA)", "Tilt (RNA)","Twist (RNA)") entries.
#'
#'
#' @param threshold is a number between (0 , 1]. In selectedIdx, indices with a correlation
#' higher than the threshold will be deleted. The default value is 1.
#'
#'
#' @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).
#'
#' @param outFormat (output format) can take two values: 'mat'(matrix) and 'txt'. The default value is 'mat'.
#'
#' @param outputFileDist shows the path and name of the 'txt' output file.
#'
#' @return The output depends on the outFormat parameter which can be either 'mat' or 'txt'. If outFormat is 'mat', the function returns a feature
#' matrix for sequences with the same length such that the number of columns is (sequence length-1)*(number of selected di-ribonucleotide indexes)
#' and the number of rows is equal to the number of sequences.
#' If the outFormat is 'txt', the output is written to a tab-delimited file.
#'
#'
#' @export
#'
#' @examples
#'
#' fileLNC<-system.file("extdata/Carica_papaya101RNA.txt",package="ftrCOOL")
#' vect<-DiNUCindex_RNA(seqs = fileLNC,outFormat="mat")



DiNUCindex_RNA<- function(seqs,selectedIdx=c("Rise (RNA)", "Roll (RNA)", "Shift (RNA)", "Slide (RNA)", "Tilt (RNA)","Twist (RNA)"),threshold=1,label=c(),outFormat="mat",outputFileDist="")
{

  path.pack=system.file("extdata",package="ftrCOOL")
  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.")
  }

  lenSeqs<-sapply(seqs, nchar)

  numSeqs<-length(seqs)



  #nucIdxAd<-paste0(path.pack,"/nuIdx2.csv")
  nucIdxAd<-paste0(path.pack,"/DI_RNA.csv")

  nucIdx<-read.csv(nucIdxAd)
  # if(standardized==TRUE){
  #
  #   nucIdxAd<-paste0(path.pack,"/standardizeNUCidx2.csv")
  #   nucIdx<-read.csv(nucIdxAd)
  # }

  row.names(nucIdx)<-nucIdx[,1]
  nucIdx<-nucIdx[selectedIdx,-1]
  nucIdx<-as.matrix(nucIdx)
  nucIdx<-type.convert(nucIdx)


  ###deleteing high correlate features
  if(threshold<1){
    nucIdx<-t(nucIdx)
    corr<-cor(nucIdx)
    corr2<-corr^2

    tmp<-corr2
    tmp[upper.tri(tmp)]<-0

    for(i in 1:ncol(tmp)){
      tmp[i,i]=0
    }

    TFidx<-apply(tmp,2,function(x) any(x > threshold))
    DlIDX<-which(TFidx==TRUE)
    RMIDX<-which(TFidx==FALSE)


    if(length(DlIDX)!=0){
      delPropName<-names(DlIDX)
      delPropName<-toString(delPropName)
      warMessage<-paste("The properties (",delPropName,") were deleted. They had a correlation with other properties more than the threshold ")
      message(warMessage)
    }

    nucIdx<- nucIdx[,RMIDX]
    nucIdx<- t(nucIdx)
  }

  if(outFormat=="mat"){
    len<-lenSeqs[1]-1
    if(length(unique(lenSeqs))>1){
      stop("ERROR: All sequences should have the same length in 'mat' mode. For sequences with different lengths, please use 'txt' for outFormat parameter")
    }
    dimFeaVct <-nrow(nucIdx)*len
    featureMatrix=matrix(0,nrow = numSeqs,ncol = dimFeaVct)


    tempname<-rep(1:len,each=nrow(nucIdx))
    temp2name<-rep(row.names(nucIdx),len)
    colna<-paste0(temp2name,"-pos",tempname)
    colnames(featureMatrix)<-colna

    for(n in 1:numSeqs){
      seq<-seqs[n]
      chars<-unlist(strsplit(seq,NULL))
      t1<-chars[1:len]
      t2<-chars[2:(len+1)]
      twoMer<-paste0(t1,t2)
      Matselected<-nucIdx[,twoMer]
      vect<-as.vector(Matselected)
      featureMatrix[n,]<-t(vect)


    }
    if(length(label)==numSeqs){
      featureMatrix<-as.data.frame(featureMatrix)
      featureMatrix<-cbind(featureMatrix,label)
    }
    row.names(featureMatrix)<-names(seqs)
    return(featureMatrix)
  }
  else{
    nameSeq<-names(seqs)
    for(n in 1:numSeqs){
      seq<-seqs[n]
      chars<-unlist(strsplit(seq,split = ""))
      len<-length(chars)-1
      t1<-chars[1:len]
      t2<-chars[2:(len+1)]
      twoMer<-paste0(t1,t2)
      Matselected<-nucIdx[,twoMer]
      vect<-as.vector(Matselected)
      Matselected<-as.character(Matselected)
      temp<-c(nameSeq[n],Matselected)
      temp<-paste(temp,collapse = "\t")
      write(temp,outputFileDist,append = TRUE)

    }
  }


}