Hi,

I am using the latest CAGEr (1.22.1) in R 3.5.0

When following the demo in CAGEr website, I found the consensusClusterGR function didn't return dominant CTSS information when specifying sample name:

> consensusClustersGR( ce, sample = "zf_unfertilized_egg", returnInterquantileWidth = TRUE, qLow = 0.1, qUp = 0.9)

The output is exactly the same as the output in the demo webpage, no dominant CTSS. Furthermore, when exporting consensusCluster to bed file:

> exportToBed(object = ce, what = "consensusClusters", qLow = 0.1, qUp = 0.9,oneFile=FALSE)

I got such error message: Error in consensusClustersQuantileLow(object) : Not supported for ‘CAGEexp’ objects. Use ‘consensusClustersQuantile()’ instead.

Then I tried with the original CAGEr format, CAGEset. There was still no dominant ctss info when calling consensusClusterGR function. Again error messge when exporting consensusCluster to bed files.

> exportToBed(object = ce, what = "consensusClusters", qLow = 0.1, qUp = 0.9, oneFile = FALSE)
Error in dominant_ctss_start[clusters.q$dominant_ctss == clusters.q$start] <- clusters.q$start[clusters.q$dominant_ctss ==  : 
  NAs are not allowed in subscripted assignments

Did I miss some critical step before exporting consensus clusters? Thanks for your help.

Best,
Jingwen