This code is to statistically test whether two genomic features are related.
The R-package regioneR v1.8 (Gel et al., 2016; R Core Team, 2016) was used to test resistance genes and genes exhibiting PAV and transposable elements for association using 500 permutations.
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For PAV association, the evaluation function numOverlaps was used to check whether the number of gene overlaps is higher than expected.
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For TE association, the evaluation function meanDistance was used since we do not expect TEs to overlap with RGA candidates due to repeats having been masked during the annotation process
the bed format of promoter
the bed format of chromosome length
- run this code and u will got the p value!