Comments (2)
nsheff
commented on July 24, 2024
Interesting. I have never tried to do an analysis like this. There is no simple way to do it, your method seems to be the best to me at the moment.
Do you have a suggestion for how such a thing could work more easily?
The only other approach I can think of is to just do your enrichments on the region sets while separated, but then combine their support, b, c, d values as you want and re-run the fisher's test on the combination. It wouldn't be exactly right due to multiple overlaps, though (some things could get counted twice). It may still work depending on the exact datasets.
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nsheff
commented on July 24, 2024
Ok, seems possible. I'll keep this on the back burner and next time I work on LOLA I'll take a look at it.
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Related Issues (20)
- hg38 database HOT 1
- Add in missing cellType/antibody entries for encodeTFBSmm10 HOT 6
- Re-order result columns
- Different results between LOLAweb interactive server and local R package HOT 7
- Inclusion of mm10 JASAPR prediction track into LOLA JASPAR HOT 3
- cistrome_mm10 HOT 2
- runLOLA results table for PEP databases
- PEP file read caching HOT 2
- Can't load an example regionDB. HOT 3
- PEP tag system
- testing for enrichment of significant individual cpgs HOT 2
- Error if GRangesList has names HOT 2
- question: how to test two region sets for differential enrichment with buildRestrictedUniverse? HOT 2
- Each of the 2 combined objects has sequence levels not in the other: HOT 4
- R package error HOT 4
- LOLA runLOLA-regionDB to use for tissue-specific TFBS
- P4 tool not grouping according to the paper!!
- Error by using extractEnrichmentOverlap function
- Fisher test - two sided hypothesis
- Error when trying to load a regionDB
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