R/pedfile.R

In snpStats: SnpMatrix and XSnpMatrix classes and methods

read.pedfile <- function(file, n, snps, which, split="\t| +", sep=".",
                        na.strings="0", lex.order=FALSE) {
  ## Constants
  r0 <- as.raw(0)
  r1 <- as.raw(1)
  r2 <- as.raw(2)
  r3 <- as.raw(3)
  ## Input file
  con <- gzfile(file)
  open(con)
  ## If no line count, find out
  if (missing(n)) {
    n <- 0
    repeat {
      line <- readLines(con, n=1)
      if (length(line)==0) break;
      n  <- n+1;
    }
    if (n==0)
      stop("Nothing read")
    seek(con, 0)
  }
  ## Find snp names
  gen <- missing(snps)
  map <- NULL
  if (!gen) {
    m <- length(snps)
    if (m==1) {
      map <- read.table(snps, comment.char="")
      m <- nrow(map)
      if (missing(which)) {
        which <- 1
        repeat {
          snps <- map[,which]
          if (!any(duplicated(snps)))
            break
          if (which==ncol(map))
            stop("No unambiguous snp names found on file")
          which <- which+1
        }
      }
      else {
        snps <- map[,which]
      }
    }
  }
  else {
    line <- readLines(con, n=1)
    fields <- strsplit(line, split)[[1]]
    nf <- length(fields)
    if (nf%%2!=0)
      stop("Odd number of fields")
    m <- (nf - 6)/2
    seek(con, 0)
  }
  nf <- 6+2*m
  ## Generate empty matrix
  result <- matrix(raw(n*m), nrow=n)
  ## Columns of subject dataframe
  ped <- character(n)
  mem <- character(n)
  pa <- character(n)
  ma <- character(n)
  sex <- numeric(n)
  aff <- numeric(n)
  rownms <- character(n)
  a1 <- a2 <- rep(NA, m)
  a1m <- a2m <- rep(TRUE, m)
  mallelic <- rep(FALSE, m) ## Multiallelic?
  for (i in 1:n) {
    line <- readLines(con, n=1)
    fields <- strsplit(line, "\t| +")[[1]]
    to.na <- fields %in% na.strings
    fields[to.na] <- NA
    ped[i] <- fields[1]
    mem[i] <- fields[2]
    pa[i] <- fields[3]
    ma[i] <- fields[4]
    sex[i] <- as.numeric(fields[5])
    aff[i] <- as.numeric(fields[6])
    alleles <- matrix(fields[7:nf], byrow=TRUE, ncol=2)
    one <- two <- rep(FALSE, m)
    for (k in 1:2) {
      ak <- alleles[,k]
      akm <- is.na(ak) 
      br1 <- !akm & a1m
      a1[br1] <- ak[br1]
      a1m[br1] <- FALSE
      br2 <- !akm & (a1==ak)
      one[br2] <- TRUE
      br3 <- !akm & !a1m & (a1!=ak)
      br4 <- br3 & a2m
      a2[br4] <- ak[br4]
      a2m[br4] <- FALSE
      br5 <- br3 & (a2==ak)
      two[br5] <- TRUE
      mallelic <- mallelic | !(akm|one|two)
    }
    gt <- rep(r0, m)
    gt[one&!two] <- r1
    gt[one&two] <- r2
    gt[two&!one] <- r3
    result[i,] <- gt
  }
  close(con)
  ## Warnin messages
  if (any(a1m))
    warning("no data for ", sum(a1m), " loci")
  mono <-(a2m & !a1m) 
  if (any(mono))
    warning(sum(mono), " loci were monomorphic")
  if (any(mallelic)) {
    result[,mallelic] <- r0;
    warning(sum(mallelic), " loci were multi-allelic --- set to NA")
  }
  ## SnpMatrix result
  if (gen)
    snps <- paste("locus", 1:m, sep=sep)
  if (any(duplicated(ped))) {
    if (any(duplicated(mem))) {
      rnames <- paste(ped, mem, sep=sep)
      if (any(duplicated(rnames)))
        stop("could not create unique subject identifiers")
    }
    else 
      rnames <- mem
  } 
  else
    rnames <- ped
  dimnames(result) <- list(rnames, snps)
  result <- new("SnpMatrix", result)
  ## Switch alleles if requested and necessary
  if (lex.order) {
    swa<- (!(is.na(a1)|is.na(a2)) & (a1>a2))
    switch.alleles(result, swa)
    a1n <- a1
    a1n[swa] <- a2[swa]
    a2[swa] <- a1[swa]
    a1 <- a1n
  }
  ## Subject support file
  fam <- data.frame(row.names=rnames, pedigree=ped, member=mem,
                    father=pa, mother=ma, sex=sex, affected=aff)
  ## map data frame 
  if (is.null(map))
    map <- data.frame(row.names=snps, snp.name=snps,
                      allele.1=a1, allele.2=a2)
  else {
    map$allele.1 <- a1
    map$allele.2 <- a2
    names(map)[which] <- "snp.names"
  }
  list(genotypes=result, fam=fam, map=map)    
}