filterflags.R

# filter flags
ff <- function(f, flags){
  ## if !all(dim(mat) == dim(flags)) break say "data and flags must have identical dimensions"
  for(k in 1:ncol(f)){
    idx.flags <- which( flags[,k] < 0 )
    f[idx.flags,k] <- NA
    cat("Number features filtered on slide ", k, ": ", length(idx.flags), "\n", sep="")
  }
  f
}