R/biSites.R

In kullrich/distIUPAC: calculates IUPAC distances on Biostrings DNAStringSet and BStringSet objects

#' @title biSites
#' @name biSites
#' @description This function returns bi-allelic site positions given a
#' dna object \code{DNAStringSet}, also with IUPAC code.
#' @import Biostrings
#' @import foreach
#' @import doMC
#' @importFrom stats as.dist sd
#' @importFrom utils combn read.table setTxtProgressBar txtProgressBar
#' @param dna \code{DNAStringSet} [mandatory]
#' @param x.pos population X positions [default: NULL]
#' @param min.ind minimum number of individuals without gaps ("-", "+", ".")
#' or without missing sites ("N"), set to size of population ("length(x.pos)")
#' to mask global deletion sites [default: 0]
#' @param wlen sliding window length [default: 25000]
#' @param start.by optional start position [default: 1]
#' @param end.by optional end position [default: NULL]
#' @param threads number of parallel threads [default: 1]
#' @param pB specifies if progress should be shown as a progress bar
#'   [default: FALSE]
#' @seealso \code{\link[distIUPAC]{triSites}},
#' \code{\link[distIUPAC]{globalDeletion}}
#' @examples
#' ##load sequence data
#' data("MySequences", package="distIUPAC")
#' 
#' ##consider all sequences
#' MySequences.biSites<-biSites(MySequences)
#' as.matrix(MySequences)[, head(MySequences.biSites$biPOS)]
#' 
#' ##consider only a subset of all sequences
#' CAS.pos<-5:34
#' CAS.biSites<-biSites(MySequences, x.pos=CAS.pos)
#' as.matrix(MySequences[CAS.pos])[, head(CAS.biSites$biPOS)]
#' 
#' ##consider only sites were 15 individuals have no gaps or missing sites
#' CAS.biSites.minInd.15<-biSites(MySequences, x.pos=CAS.pos, min.ind=15)
#' as.matrix(MySequences[CAS.pos])[, head(CAS.biSites.minInd.15$biPOS)]
#' as.matrix(MySequences[CAS.pos])[, head(CAS.biSites.minInd.15$biPOSmasked)]
#' @export biSites
#' @author Kristian K Ullrich
biSites<-function(dna, x.pos=NULL, min.ind=0, wlen=25000, start.by=1,
  end.by=NULL, threads=1, pB=FALSE){
    IUPAC_CODE_MAP_LIST<-list( c("A"), c("C"), c("G"), c("T"),
      c("A","C"), c("A","G"), c("A","T"), c("C","G"), c("C","T"), c("G","T"), 
      c("A","C","G"), c("A","C","T"), c("A","G","T"), c("C","G","T"),
      c(), c(), c(), c() )
    names(IUPAC_CODE_MAP_LIST)<-c("A", "C", "G", "T", 
      "M", "R", "W", "S", "Y", "K", "V",
      "H", "D", "B", "N", "-", "+", ".")
    options(scipen=22)
    if(is.null(end.by)){end.by<-unique(width(dna))}
    if(start.by>unique(width(dna))){stop("start.by needs to be equal or
      smaller than dna length")}
    if(end.by>unique(width(dna))){stop("end.by needs to be equal or
      smallerthan dna length")}
    if(is.null(x.pos)){
        x.pos<-seq(1,length(dna))
    }
    dna_<-dna[x.pos]
    x.pos_<-seq(1, length(x.pos))
    tmp.sw<-swgen(wlen=wlen, wjump=wlen, start.by=start.by, end.by=end.by)
    if(pB){
        pb<-txtProgressBar(min=0, max=ncol(tmp.sw), initial=0, style=3)
    }
    j<-NULL
    registerDoMC(threads)
    OUT<-foreach(j=seq(from=1, to=ncol(tmp.sw)), .combine=rbind) %dopar% {
        START<-tmp.sw[1, j][[1]]
        END<-tmp.sw[2, j][[1]]
        biPOSall<-NA
        biPOS<-NA
        biPOSmasked<-NA
        minIndPOS<-NA
        tmp.seq<-subseq(dna_, START, END)
        cM<-consensusMatrix(tmp.seq)
        minIndPOS<-START - 1 + which(!apply(cM, 2, function(x) {
              sum(x[1:14])
          })>=min.ind)
        if(unique(width(tmp.seq))==1){
            tmp.seq.cM<-t(as.matrix(apply(cM, 1, function(x) {
                  ifelse(x>0, 1, 0)
              })))
        }
        if(unique(width(tmp.seq))!=1){
            tmp.seq.cM<-apply(cM, 1, function(x) {
                  ifelse(x>0, 1, 0)
              })
        }
        biPOSall<-START - 1 + which(apply(tmp.seq.cM, 1, function(x) {
              length(unique(unlist(unique(
                IUPAC_CODE_MAP_LIST[names(x[x==1])]
              ))))
          })==2)
        biPOS<-biPOSall[which(!biPOSall%in%minIndPOS)]
        biPOSmasked<-biPOSall[which(biPOSall%in%minIndPOS)]
        if(pB){
            setTxtProgressBar(pb, j)
        }
        list(biPOS, biPOSmasked, minIndPOS)
    }
    if(pB){
        setTxtProgressBar(pb, ncol(tmp.sw))
        close(pb)    
    }
    if(is.matrix(OUT)){
        OUT<-list(unlist(OUT[,1]), unlist(OUT[,2]), unlist(OUT[,3]))  
    }
    names(OUT)<-c("biPOS", "biPOSmasked", "minIndPOS")
    names(OUT$biPOS)<-NULL
    names(OUT$biPOSmasked)<-NULL
    names(OUT$minIndPOS)<-NULL
    return(OUT)
}