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.
| Version: | 0.99 |
| Depends: | GenomicRanges |
| Imports: | igraph, car, IRanges, parallel |
| Suggests: | knitr, rmarkdown, ggplot2 |
| Published: | 2016-03-21 |
| Author: | Musaddeque Ahmed |
| Maintainer: | Hansen He <hansenhe at uhnresearch.ca> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| CRAN checks: | VSE results |
| Reference manual: | VSE.pdf |
| Vignettes: |
Variant Set Enrichment |
| Package source: | VSE_0.99.tar.gz |
| Windows binaries: | r-devel: VSE_0.99.zip, r-release: VSE_0.99.zip, r-oldrel: VSE_0.99.zip |
| macOS binaries: | r-release: VSE_0.99.tgz, r-oldrel: not available |
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