DOI: 10.18129/B9.bioc.cpvSNP    

Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

Bioconductor version: Release (3.6)

Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.

Author: Caitlin McHugh, Jessica Larson, and Jason Hackney

Maintainer: Caitlin McHugh <mchughc at uw.edu>

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PDF R Script Running gene set analyses with the "cpvSNP" package
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biocViews GeneSetEnrichment, Genetics, GenomicVariation, Pathways, Software, StatisticalMethod
Version 1.10.0
In Bioconductor since BioC 3.1 (R-3.2) (3 years)
License Artistic-2.0
Depends R (>= 2.10), GenomicFeatures, GSEABase(>= 1.24.0)
Imports methods, corpcor, BiocParallel, ggplot2, plyr
Suggests TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle
Depends On Me
Imports Me
Suggests Me
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Source Package cpvSNP_1.10.0.tar.gz
Windows Binary cpvSNP_1.10.0.zip
Mac OS X 10.11 (El Capitan) cpvSNP_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cpvSNP
Package Short Url http://bioconductor.org/packages/cpvSNP/
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