Is the user expected to add a window around her peaks?

[holgerbrandl]

Co-localization/enrichment relies on some defined proximity window. But since the UI does not expose any such window-size, I'm wondering if we have to expand the query sets (e.g. macs2 peaks in my case) using bedtools slop (or similar)?
Or is the user supposed to upload peaks as they come from the caller, and LOLA deals with some definition of proximity internally?

[nsheff]

LOLA is going to just treat your regions exactly as you provide them. So, it assumes you've pre-processed them to be the exact size you want them to be.

It would be possible for us to make some simple resizing options. Maybe we should do that... the problem is just that it's so biology-specific, that it would be really hard to please everyone, you know?

[holgerbrandl]

Indeed it's really hard to define what vicinity really means. But pointing out the necessity of doing so before/when using LOLA would be helpful imho.

[nsheff]

@vpnagraj it actually wouldn't be too hard to add another field in the shiny app called 'padding', which could be useful. What do you think?

we would just then use this 'padding 'parameter to run a GenomicRanges::resize() call on the uploaded regions.

[vpnagraj]

@nsheff sure thing

but i'm not familiar with GenomicRanges::resize() so can you give you me a better idea of where to make that call? after reading each .bed?

and given that a user might upload multiple region sets, would the padding be the same on all files?

it would also help to know what the range of possible values (and a sensible default) for that padding value would be