Dear all,

I need to filter a QualityScaledDNAStringSet that have less than 10% of the nucleotide having a Q score less than 30.

I can get the numbers of Q scores in a list with as(quality(Set), "IntegerList")

How can I apply the calculation?

Thank you!

For some IntegerList

set.seed(123)
il = IntegerList(runif(20, 25, 40), runif(30, 25, 40))

you can perform mathematical operations that are vectorized over the elements

keep = (sum(il > 30) / lengths(il)) > .6

and then subset the original 

Set[keep]