VSE: 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.

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

Downloads:

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
OS X Mavericks binaries: r-release: VSE_0.99.tgz, r-oldrel: VSE_0.99.tgz

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