Hello, Are q0.1 and q0.9 values the same in CAGEexp and CAGEset objects? To cut a long story short, I'm trying to run a code in which they used CAGEset objects, but taking advantage of CAGEr vignette I created a CAGEexp object. the CAGEseq object value os a position of $q0.1 and $q0.9 from base n=1 of the chromosome (so big numbers close to those in $start $end columns) the CAGEexp object I created has very small values, like 1, 10, 25, they look like the distance from the base n=1 of the interval defined by start and end columns. is it like that? to get the InterquantileWidth tagClusters() should I just edit those columns by doing

 x$"q_0.1" = x$"start" + x$"q_0.1" - 1
 x$"q_0.9" = x$"start" + x$"q_0.9" - 1

many thanks !

Hello again,

CAGEset and CAGEexp objects differ in the way they internally store quantile information, by both of them should return the same values with commands such as CAGEr:::tagClustersQuantileLow(exampleCAGEexp, 1, "0.1"). (Please note that exampleCAGEexp and exampleCAGEset are not the same data).

CAGEexp objects store quantile positions relatively to the start of the cluster. This allows for efficient Rle compression, especially for small quantiles or with unfiltered clusters where many of them have a size of 1.