Hi all, 

Have a set of peaks and TSSs, trying to use the following function to retrieve the distance from peaks to nearest TSS and getting this error:

Wondering you anyone has an idea about why? Thanks!

# Get distance from peaks to the nearest TSS
tmp <- getNearestDist(all.peaks,tss,return.nearest=T)

Error in .Call2("map_positions", run_lens, pos, method, PACKAGE = "S4Vectors") : 

  subscript contains NAs

​function(gr1, gr2, return.nearest=F, r1.pos="mid", r2.pos="mid", strand=2)
{
  r1 <- ranges(gr1)
  r2 <- ranges(gr2)
  map.id <- rep(NA, length(r1))
  dist <- c()
  for(chr in sort(unique(seqnames(gr1)))){
    select1 <- seqnames(gr1)==chr
    gr1.select <- gr1[select1,]
    select2 <- seqnames(gr2)==chr
    gr2.select <- gr2[select2,]
    l <- nearest(ranges(gr1.select), ranges(gr2.select))
    map.id[which(select1)] <- which(select2)[l]

    start1=start(gr1.select)
    end1 = end(gr1.select)
    end5.1 <- start1
    end3.1 <- end1
    neg1 <- strand(gr1.select) == "-"
    end5.1[which(neg1)] <- end1[which(neg1)]     
    end3.1[which(neg1)] <- start1[which(neg1)]     
    mid1 <- as.integer( (start1+end1)/2)

    start2=start(gr2.select)
    end2 = end(gr2.select)
    end5.2 <- start2
    end3.2 <- end2
    neg2 <- strand(gr2.select) == "-"
    end5.2[which(neg2)] <- end2[which(neg2)]     
    end3.2[which(neg2)] <- start2[which(neg2)]     
    mid2 <- as.integer( (start2+end2)/2)

    pos1 <- switch(r1.pos,
                   mid=mid1,
                   start=start1,
                   end = end1,
                   end5 = end5.1,
                   end3 = end3.1)
    pos2 <- switch(r2.pos,
                   mid=mid2,
                   start=start2,
                   end = end2,
                   end5 = end5.2,
                   end3 = end3.2)            
    tmp.dist <- as.integer(pos1 - pos2[l])
    if(strand==2){
      tmp.dist[which(neg2[l])] <- - tmp.dist[which(neg2[l])]
    }     
    if(strand==1){
      tmp.dist[which(neg1)] <- - tmp.dist[which(neg1)]
    }
    dist[which(select1)] <- tmp.dist
  }
  if(!return.nearest){
    dist
  }
  else{
    gr <- gr2[map.id,]
    values(gr)$dist <- dist
    gr$map.id = map.id
    gr
  }
}​