udf_impute2mach.R

udf_impute2mach <- function(inFile=NA, outFolder=NA)
{
  # Check input -------------------------------------------------------------
  if(is.na(inFile)) stop("No input file!")
  if(!file.exists(inFile)) stop("Input file doesn't exist!")
  if(is.na(outFolder)) {
    outFolder <- getwd()
    warning("Output folder is set to working directory - getwd()")
    }

  # Workspace ---------------------------------------------------------------
  
  outFileMAP=paste0(outFolder,"/",basename(inFile),".map")
  outFileDOSE=paste0(outFolder,"/",basename(inFile),".dose")
  
  #read Impute2 output
  dat <- readLines(inFile)
  
  # Make MAP file -----------------------------------------------------------
  MAP <- 
    as.data.frame(do.call(
      rbind,
      lapply(dat,
             function(x){
               unlist(strsplit(x," "))[1:5]})))
  #output map file
  write.table(MAP,outFileMAP,quote=FALSE,row.names=FALSE,col.names=FALSE)
  
  # Make DOSE file ----------------------------------------------------------
  #write in chunks to avoid filling up memory - append to file every chunk
  chunk=1000
  for(i in seq(1,length(dat),chunk)){
    ixStart <- i
    ixEnd <- ifelse(ixStart+chunk-1 > length(dat),
                     length(dat),
                     ixStart+chunk-1)
    d_chunk <- dat[ixStart:ixEnd]
    
    #make dosage and write with append
    DOSE <-
      do.call(rbind,
              lapply(d_chunk,
                     function(x){
                       #x<-dat[1]
                       d <- unlist(strsplit(x," "))
                       d <- as.numeric(d[6:length(d)])
                       sapply(seq(1,length(d),3),function(i)
                         # Minor allele count (AA*0+AB*1+BB*2) is same as (AB + BB*2)
                         d[i+1] + d[i+2]*2)
                     }))
    
    #output dosage file
    write.table(DOSE,outFileDOSE,quote=FALSE,
                row.names=FALSE,col.names=FALSE,append=TRUE)
    
    #loop status
    flush.console()
    print(i)
  }
}