Identifying outlier loci in R
As Devon said, removing the which will give you W as a logical vector that can be used to index the sorted p-values. To get a logical vector that can be used to subset the original (unsorted) values you’ll need to go a step further:

candidates = is.element(1 : L, order(adjusted.p.values)[W])


However, I’m not sure this will work with your data: the name adjusted.p.values suggests that these values are already FDR-adjusted. So you cannot/should not perform additional correction on them. If they are already adjusted, then you can get candidate loci simply by

candidates = adjusted.p.values &lt; q