R/CkSGAApair.R

In ftrCOOL: Feature Extraction from Biological Sequences

#' Composition of k-Spaced Grouped Amino Acids pairs (CkSGAApair)
#'
#' In this function, amino acids are first grouped into a category which is defined by the user.
#' Later, the composition of the k-spaced grouped amino acids is computed.
#' Please note that this function differs from \link{CkSAApair} which works on individual amino acids.
#'
#'
#' @details Column names in the feature matrix follow G(?ss?). For example, G(1ss2) means Group1**Group2, where
#' '*' is a wild character.
#'
#'
#' @note 'upto' is enabled only when rng is a number and not a vector.
#'
#' @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 rng This parameter can be a number or a vector. Each element of the vector shows the number of spaces between amino acid pairs.
#' For each k in the rng vector, a new vector (whose size is (number of categorizes)^2) is created which contains the frequency of pairs with k gaps.
#'
#'
#' @param upto It is a logical parameter. The default value is FALSE. If rng is a number and upto is set to TRUE, rng is converted
#' to a vector with values from [1 to rng].
#'
#' @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 Grp is a list of vectors containig amino acids. Each vector represents a category. Users can define a customized amino acid grouping, provided that the sum of all amino acids is 20 and there is no repeated amino acid in the groups.
#' Also, users can choose 'cTriad'(conjointTriad), 'locFus', or 'aromatic'. Each option provides specific information about the type of an amino acid grouping.
#'
#' @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. Row length is equal to the number of sequences and
#' the number of columns is ((number of categorizes)^2)*(length of rng vector).
#'
#'
#' @export
#'
#' @examples
#'
#' filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
#' mat1<-CkSGAApair(seqs=filePrs,rng=2,upto=TRUE,Grp="aromatic")
#'
#' mat2<-CkSGAApair(seqs=filePrs,rng=c(1,3,5),upto=FALSE,Grp=
#' list(Grp1=c("G","A","V","L","M","I","F","Y","W"),Grp2=c("K","R","H","D","E")
#' ,Grp3=c("S","T","C","P","N","Q")))
#'

CkSGAApair <- function(seqs,rng=3,upto=FALSE,normalized=TRUE,Grp="locFus",label=c()){



  DictAA<-c("A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y")

  if(is.list(Grp)){
    Group = Grp
  }
  else{

  if(Grp=="locFus"){
    Group=list(Grp1=c("A","E")
               ,Grp2=c("R","Q","K","H"),Grp3=c("N","D","S","T"),Grp4=c("G"),Grp5=c("P")
               ,Grp6=c("I","L","M","F","V"),Grp7=c("W","Y"),Grp8=c("C"))
  } else if (Grp=="aromatic"){

    Group =list(Grp1=c("G","A","V","L","M","I")
                ,Grp2=c("F","Y","W"),Grp3=c("K","R","H")
                ,Grp4=c("D","E"),Grp5=c("S","T","C","P","N","Q"))

  } else if (Grp=="cTriad"){
    Group =list(Grp1=c("A","G","V" )
                ,Grp2=c("I","L","F","P"),Grp3=c("Y" ,"M","T","S")
                ,Grp4=c("H","N","Q","W"),Grp5=c("R","K"), Grp6=c("D","E")
                ,Grp7=c("C"))
  } else {
    if(!is.list(Grp)){
      stop("ERROR: Grp should be either one of 'locFus', 'aromatic', or 'cTriad' or a list containing a valid grouping of amino acids")
    }

  }
  }


  #Error in inputs (Group members are not unique)
  numGrp<-length(Group)
  grps<-unlist(Group)
  unqGrps<-unique(grps)
  if(!all(grps %in% DictAA)==TRUE){
    stop("ERROR: There is an unknown amino acid in Grp")
  }
  if (length(grps)!=length(unqGrps)){
    stop("ERROR: There is a duplicated amino acid in Grp")
  }
  if(length(grps)!=20)
  {
    stop("ERROR: Total number of amino acids in Grp should be 20 exactly")
  }


  #read sequences
  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)


  aa<-vector()

  VectGrp<-c("Grp10"='a',"Grp11"='b',"Grp12"='c',"Grp13"='d',"Grp14"='e',"Grp15"='f',"Grp16"='g',"Grp17"='h',"Grp18"='i',"Grp19"='j',"Grp20"='k')

  for (i in 1:numGrp)
  {
    if(i<10){
      vect<-rep(i,length(Group[[i]]))
      aa<-c(aa,vect)
    } else if(i<=20){
      aa<-c(aa,rep(VectGrp[(i-9)],length(Group[[i]])))
    }
  }

  names(aa)<-grps

  if(upto==TRUE && length(rng)==1){
    l<-length(rng)
    l<-rng[l]
    rng<-0:l
  }

  rng <- sort(rng)
  len<-length(rng)


  dipep<-nameKmer(k=2,type = "num",numGrp)



  seqChars<-lapply(seqs,function(seq){unlist(strsplit(seq,split = ""))})
  GrpSeqs<-lapply(seqChars,function(seq){aa[seq]})
  lenSeqs<-lapply(seqs,nchar)

  featureMatrix<-c()

  numcol=numGrp^2

  for(i in 1:len){
    tempMat<-matrix(0,nrow = numSeqs,ncol = numcol)
    colnames(tempMat)<-dipep
    for(n in 1:numSeqs)
    {
      temp1<-GrpSeqs[[n]][1:(lenSeqs[[n]]-rng[i]-1)]
      temp2<-GrpSeqs[[n]][((rng[i]+1)+1):(lenSeqs[[n]])]
      kmers<-paste(temp1,temp2,sep = "")
      tbkmers<-table(kmers)
      tempMat[n,names(tbkmers)]<-tbkmers
    }
    featureMatrix<-cbind(featureMatrix,tempMat)

  }

  for(i in 1:length(dipep)){
    ditemp<-unlist(strsplit(dipep[i],split = ""))
    dipep[i]<-paste(ditemp[1],ditemp[2])
  }


  featName<-vector()
  for(i in 1:len){
    featName<-c(featName,gsub(" ",strrep("s",rng[i]),dipep))
  }
  featName<-paste0("G(",featName,")")

  colnames(featureMatrix)<-featName


  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)
}