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]))
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