qtl: Tools for analyzing QTL experiments

######################################################################
#
# read.cross.gary.R
#
# copyright (c) 2000-2011, Karl W Broman
# last modified May, 2011
# first written Aug, 2000
#
#     This program is free software; you can redistribute it and/or
#     modify it under the terms of the GNU General Public License,
#     version 3, as published by the Free Software Foundation.
# 
#     This program is distributed in the hope that it will be useful,
#     but without any warranty; without even the implied warranty of
#     merchantability or fitness for a particular purpose.  See the GNU
#     General Public License, version 3, for more details.
# 
#     A copy of the GNU General Public License, version 3, is available
#     at http://www.r-project.org/Licenses/GPL-3
#
# Part of the R/qtl package
# Contains: read.cross.gary
#           [See read.cross.R for the main read.cross function.]
#
######################################################################

######################################################################
#
# read.cross.gary
#
# read data in Gary's format
#
######################################################################

read.cross.gary <-
function(dir,genfile,mnamesfile,chridfile,phefile,pnamesfile,mapfile,
         estimate.map,na.strings)
{
  # create file names
  if(missing(genfile)) genfile <- "geno.dat"
  if(missing(mnamesfile)) mnamesfile <- "mnames.txt"
  if(missing(chridfile)) chridfile <- "chrid.dat"
  if(missing(phefile)) phefile <- "pheno.dat"
  if(missing(pnamesfile)) pnamesfile <- "pnames.txt"
  if(missing(mapfile)) mapfile <- "markerpos.txt"

  if(!missing(dir) && dir != "") {
    genfile <- file.path(dir, genfile)
    mnamesfile <- file.path(dir, mnamesfile)
    chridfile <- file.path(dir, chridfile)
    phefile <- file.path(dir, phefile)
    if(!is.null(pnamesfile)) pnamesfile <- file.path(dir, pnamesfile)
    if(!is.null(mapfile)) mapfile <- file.path(dir, mapfile)
  }

  # read data
  allgeno <- as.matrix(read.table(genfile,na.strings="9"))+1
  pheno <- as.matrix(read.table(phefile,na.strings=na.strings,header=FALSE))
  chr <- scan(chridfile,what=character(),quiet=TRUE)
  mnames <- scan(mnamesfile,what=character(),quiet=TRUE)

  if(!is.null(mapfile)) {
    map <- read.table(mapfile,row.names=1)
    map <- map[mnames,1]
    map.included <- TRUE
  }
  else {
    map <- seq(0,by=5,len=length(mnames))
    map.included <- FALSE
  }

  if(!is.null(pnamesfile)) pnames <- scan(pnamesfile,what=character(),quiet=TRUE)
  else pnames <- paste("pheno",1:ncol(pheno),sep="")


  # fix up map information
  # number of chromosomes
  uchr <- unique(chr)
  n.chr <- length(uchr)
  geno <- vector("list",n.chr)
  names(geno) <- uchr
  min.mar <- 1
  for(i in 1:n.chr) { # loop over chromosomes
    # create map
    temp.map <- map[chr==uchr[i]]

    # deal with any markers that didn't appear in the marker pos file
    if(any(is.na(temp.map))) {
      o <- (seq(along=temp.map))[is.na(temp.map)]
      for(j in o) {
        if(j==1 || all(is.na(temp.map[1:(j-1)]))) {
          z <- min((seq(along=temp.map))[-o])
          temp.map[j] <- min(temp.map,na.rm=TRUE)-(z-j+1)
        }
        else if(j==length(temp.map) || all(is.na(temp.map[-(1:j)]))) {
          z <- max((seq(along=temp.map))[-o])
          temp.map[j] <- max(temp.map,na.rm=TRUE)+(j-z+1)
        }
        else {
          temp.map[j] <- (min(temp.map[-(1:j)],na.rm=TRUE)+
                          max(temp.map[1:(j-1)],na.rm=TRUE))/2
        }
      }
    }

    names(temp.map) <- mnames[chr==uchr[i]]

    # pull out appropriate portion of genotype data
    data <- allgeno[,min.mar:(length(temp.map)+min.mar-1),drop=FALSE]
    min.mar <- min.mar + length(temp.map)
    colnames(data) <- names(temp.map)

    geno[[i]] <- list(data=data,map=temp.map)
    if(uchr[i] == "X" || uchr[i] == "x")
      class(geno[[i]]) <- "X"
    else class(geno[[i]]) <- "A"
  }
  colnames(pheno) <- pnames

  # fix up phenotype data: make things numeric that look numeric
  sw2numeric <-
    function(x) {
      pattern <- "^[ \t]*-*[0-9]*[.]*[0-9]*[ \t]*$"
      n <- sum(!is.na(x))
      if(length(grep(pattern,as.character(x[!is.na(x)])))==n)
        return(as.numeric(as.character(x)))
      else return(x)
    }
  pheno <- data.frame(lapply(as.data.frame(pheno), sw2numeric), stringsAsFactors=TRUE)

  # check that data dimensions match
  n.mar1 <- sapply(geno,function(a) ncol(a$data))
  n.mar2 <- sapply(geno,function(a) length(a$map))
  n.phe <- ncol(pheno)
  n.ind1 <- nrow(pheno)
  n.ind2 <- sapply(geno,function(a) nrow(a$data))
  if(any(n.ind1 != n.ind2)) {
    cat(n.ind1,n.ind2,"\n")
    stop("Number of individuals in genotypes and phenotypes do not match.");
  }
  if(any(n.mar1 != n.mar2)) {
    cat(n.mar1,n.mar2,"\n")
    stop("Numbers of markers in genotypes and marker names files do not match.");
  }

  # print some information about the amount of data read
  cat(" --Read the following data:\n");
  cat("\t", n.ind1, " individuals\n");
  cat("\t", sum(n.mar1), " markers\n");
  cat("\t", n.phe, " phenotypes\n");

  # determine map type: f2 or bc or 4way?
  if(max(allgeno[!is.na(allgeno)])<=2) type <- "bc"
  else type <- "f2"
  cross <- list(geno=geno,pheno=pheno)
  class(cross) <- c(type,"cross")

  # check that nothing is strange in the genotype data
  cross.type <- class(cross)[1]
  if(cross.type=="f2") max.gen <- 5
  else max.gen <- 2

  u <- unique(allgeno)
  if(any(!is.na(u) & (u > max.gen | u < 1))) 
    stop("There are stange values in the genotype data : ",
                 paste(sort(u),collapse=":"), ".")

  cross$pheno <- as.data.frame(cross$pheno, stringsAsFactors=TRUE)

  # if map wasn't included, go through each chromosome and
  # make first marker at 0 cM.
  if(!map.included) {
    for(i in 1:nchr(cross))
      cross$geno[[i]]$map <- cross$geno[[i]]$map - min(cross$geno[[i]]$map)
  }

  # return cross + indicator of whether to run est.map
  # [run est.map if map not included and estimate.map == TRUE]
  list(cross, (!map.included && estimate.map) )
}

# end of read.cross.gary.R