added interval functionality to LinkPeaks

[kmwinkley]

Hi Tim,

I've got another PR here for some added functionality to the LinkPeaks methods. We're in a situation where we'd like to look at potential very long-range enhancers (> 500kb and < 1mb) across the whole genome, but we've already called linked peaks using the default 500 kb distance. We'd like to avoid re-running the peak-gene linkage on all the peaks within 500 kb of the TSS and only search in our defined interval. This commit allows users to specify a minimum distance for the peak from the TSS along with the already included maximum distance from TSS. I think people will potentially find it useful for enhancer searches by allowing them to exclude promoter regions, or to search a defined interval for a specific gene, along with other use cases.

[timoast]

Thanks for the PR! This is certainly a useful feature, especially to exclude testing gene promoters