Variant Set Enrichment

Calculates the enrichment of associated variant set (AVS) for an array of genomic regions. The AVS is the collection of disjoint LD blocks computed from a list of disease associated SNPs and their linked (LD) SNPs. VSE generates a null distribution of matched random variant sets (MRVSs) from 1000 Genome Project Phase III data that are identical to AVS, LD block by block. It then computes the enrichment of AVS intersecting with user provided genomic features (e.g., histone marks or transcription factor binding sites) compared with the null distribution.


Reference manual

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0.99 by Hansen He, 4 years ago

Browse source code at

Authors: Musaddeque Ahmed <[email protected]>

Documentation:   PDF Manual  

GPL-3 license

Imports igraph, car, IRanges, parallel

Depends on GenomicRanges

Suggests knitr, rmarkdown, ggplot2

See at CRAN