Conservation analysis (site_cons) fails

[KrRi4]

Hi, I tried running your tutorial, but ran into the following issue when running the conservation analysis. Any suggestions on getting this to work would be appreciated!

Note, that the object can be viewed as it is already in the tutorial, however, using the listed commands it fails.

Thanks, Kris

> xs <- findOverlaps(sites, cons)
> site_cons <- sapply(1:length(sites), function(i) {
+   # Conservation scores for each positions in a PWM match.
+   ys <- cons[subjectHits(xs[queryHits(xs) == i])]
+   vals <- rep(ys$score, width(ys))
+   idx <- seq(
+     from = start(sites[i]) - min(start(ys)) + 1,
+     length.out = width(sites[i])
+   )
+   vals <- vals[idx]
+   mean(vals)
+ })
Error in seq.default(from = start(sites[i]) - min(start(ys)) + 1, length.out = width(sites[i])) : 
  'from' must be a finite number
In addition: Warning message:
In min(start(ys)) : no non-missing arguments to min; returning Inf
Called from: seq.default(from = start(sites[i]) - min(start(ys)) + 1, length.out = width(sites[i]))

[slowkow]

Looks like min(start(ys)) is returning Inf (infinity):

In min(start(ys)) : no non-missing arguments to min; returning Inf

You might consider double-checking that you have the correct data in sites and cons.