VSE: Variant Set Enrichment

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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.

Author
Musaddeque Ahmed <musa.ahmed@utoronto.ca>
Date of publication
2016-03-21 23:10:53
Maintainer
Hansen He <hansenhe@uhnresearch.ca>
License
GPL-3
Version
0.99

View on CRAN

Man pages

avsSize
avsSize
bedToGRanges
bedToGRanges
intersectMatrix
intersectMatrix
loadLd
loadLd
loadSampleRegions
loadSampleRegions
makeAVS
makeAVS
makeMRVS
makeMRVS
variantSetEnrichment
variantSetEnrichment
VSEplot
VSEplot
VSEqq
VSEqq
VSESummary
VSESummary

Files in this package

VSE
VSE/inst
VSE/inst/extdata
VSE/inst/extdata/ld_BCa_raggr.csv
VSE/inst/extdata/vse_output.Rda
VSE/inst/extdata/bca.mrvs.200.Rda
VSE/inst/doc
VSE/inst/doc/my-vignette.html
VSE/inst/doc/my-vignette.Rmd
VSE/inst/doc/my-vignette.R
VSE/NAMESPACE
VSE/R
VSE/R/loadSampleRegions.R
VSE/R/bedToGRanges.R
VSE/R/VSESummary.R
VSE/R/makeMRVS.R
VSE/R/makeAvs.R
VSE/R/VSEplot.R
VSE/R/avsSize.R
VSE/R/intersectMatrix.R
VSE/R/VSEqq.R
VSE/R/loadLd.R
VSE/R/variantSetEnrichment.R
VSE/vignettes
VSE/vignettes/my-vignette.Rmd
VSE/MD5
VSE/build
VSE/build/vignette.rds
VSE/DESCRIPTION
VSE/man
VSE/man/VSEplot.Rd
VSE/man/loadLd.Rd
VSE/man/VSESummary.Rd
VSE/man/makeAVS.Rd
VSE/man/bedToGRanges.Rd
VSE/man/makeMRVS.Rd
VSE/man/intersectMatrix.Rd
VSE/man/avsSize.Rd
VSE/man/loadSampleRegions.Rd
VSE/man/variantSetEnrichment.Rd
VSE/man/VSEqq.Rd