cpvSNP: Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Version 1.8.0

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.

AuthorCaitlin McHugh, Jessica Larson, and Jason Hackney
Bioconductor views GeneSetEnrichment Genetics GenomicVariation Pathways StatisticalMethod
Date of publicationNone
MaintainerCaitlin McHugh <mchughc@uw.edu>
LicenseArtistic-2.0
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cpvSNP")

Popular man pages

createArrayData: Create a GRanges Object for a GWAS data.frame
geneSetAnalysis: Data to run gene set analysis methods
geneToSNPList: Translate a List of Gene Ids to Their Corresponding SNP Ids
GLOSSIResultCollection-class: Class '"GLOSSIResultCollection"'
vegas: Calculate the P-Value for a Set Using the VEGAS Method
vegasMarginal: Calculate the P-Value for a Set Using the VEGAS Method
VEGASResult-class: Class '"VEGASResult"'
See all...

All man pages Function index File listing

Man pages

assocPvalBySetPlot: Create a Density Plot of P-Values, Highlighting SNPs Within a...
createArrayData: Create a GRanges Object for a GWAS data.frame
degreesOfFreedom-method: ~~ Methods for Function 'degreesOfFreedom' ~~
exampleArrayData: SNP Array Data to Use for Gene Set Analysis
geneSetAnalysis: Data to run gene set analysis methods
geneSetName-methods: ~~ Methods for Function 'geneSetName' ~~
GeneSetResult-class: Class '"GeneSetResult"'
GeneSetResultCollection-class: Class '"GeneSetResultCollection"'
geneSets: Gene Set Collection object
geneToSNPList: Translate a List of Gene Ids to Their Corresponding SNP Ids
glossi: Calculate a Chi-squared Statistic and P-Value for Independent...
glossiMarginal: Calculate a Chi-squared Statistic and P-Value for Items in a...
GLOSSIResult-class: Class '"GLOSSIResult"'
GLOSSIResultCollection-class: Class '"GLOSSIResultCollection"'
plotPvals: Create a Plot of P-Values Against Number of SNPs per Set for...
pValue-method: ~~ Methods for Function 'pValue' ~~
show-methods: ~~ Methods for Function 'show' in Package 'base' ~~
simulate_chisq: Simulate a Chi-squared Statistic from a Distribution with a...
simulatedStats-method: ~~ Methods for Function 'simulatedStats' ~~
statistic-methods: ~~ Methods for Function 'statistic' ~~
vegas: Calculate the P-Value for a Set Using the VEGAS Method
vegasMarginal: Calculate the P-Value for a Set Using the VEGAS Method
VEGASResult-class: Class '"VEGASResult"'
VEGASResultCollection-class: Class '"VEGASResultCollection"'

Functions

GLOSSIResult-class Man page
GLOSSIResultCollection-class Man page
GeneSetResult-class Man page
GeneSetResultCollection-class Man page
VEGASResult-class Man page
VEGASResultCollection-class Man page
assocPvalBySetPlot Man page Source code
createArrayData Man page Source code
degreesOfFreedom Man page
degreesOfFreedom,GLOSSIResult-method Man page
degreesOfFreedom,GLOSSIResultCollection-method Man page
degreesOfFreedom,GeneSetResult-method Man page
degreesOfFreedom,GeneSetResultCollection-method Man page
degreesOfFreedom,VEGASResult-method Man page
degreesOfFreedom,VEGASResultCollection-method Man page
degreesOfFreedom-methods Man page
exampleArrayData Man page
geneSetAnalysis Man page
geneSetName Man page
geneSetName,GLOSSIResult-method Man page
geneSetName,GLOSSIResultCollection-method Man page
geneSetName,GeneSetResult-method Man page
geneSetName,GeneSetResultCollection-method Man page
geneSetName,VEGASResult-method Man page
geneSetName,VEGASResultCollection-method Man page
geneSetName-methods Man page
geneSets Man page
geneToSNPList Man page Source code
glossi Man page Source code
glossiMarginal Man page Source code
pValue Man page
pValue,GLOSSIResult-method Man page
pValue,GLOSSIResultCollection-method Man page
pValue,GeneSetResult-method Man page
pValue,GeneSetResultCollection-method Man page
pValue,VEGASResult-method Man page
pValue,VEGASResultCollection-method Man page
pValue-methods Man page
plotPvals Man page Source code
show Man page
show,GLOSSIResult-method Man page
show,VEGASResult-method Man page
show-methods Man page
simulate_chisq Man page Source code
simulatedStats Man page
simulatedStats,VEGASResult-method Man page
simulatedStats,VEGASResultCollection-method Man page
simulatedStats-methods Man page
statistic Man page
statistic,GLOSSIResult-method Man page
statistic,GLOSSIResultCollection-method Man page
statistic,GeneSetResult-method Man page
statistic,GeneSetResultCollection-method Man page
statistic,VEGASResult-method Man page
statistic,VEGASResultCollection-method Man page
statistic-methods Man page
vegas Man page Source code
vegasMarginal Man page Source code
vegasPrep Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/GLOSSIResult-accessors.R
R/GeneSetResult-accessors.R
R/VEGASResult-accessors.R
R/assocPvalBySetPlot.R
R/createArrayData.R
R/geneToSNPList.R
R/glossi.R
R/glossiMarginal.R
R/plotPvals.R
R/show-methods.R
R/simulate_chisq.R
R/vegas.R
R/vegasMarginal.R
R/vegasPrep.R
build
build/vignette.rds
data
data/datalist
data/geneSetAnalysis.RData
data/test_genesHg19.RData
data/test_snpsGSC.RData
inst
inst/doc
inst/doc/cpvSNP.R
inst/doc/cpvSNP.Rnw
inst/doc/cpvSNP.pdf
inst/unitTests
inst/unitTests/test_cpvSNP.R
man
man/GLOSSIResult-class.Rd
man/GLOSSIResultCollection-class.Rd
man/GeneSetResult-class.Rd
man/GeneSetResultCollection-class.Rd
man/VEGASResult-class.Rd
man/VEGASResultCollection-class.Rd
man/assocPvalBySetPlot.Rd
man/createArrayData.Rd
man/degreesOfFreedom-method.Rd
man/exampleArrayData.Rd
man/geneSetAnalysis.Rd
man/geneSetName-methods.Rd
man/geneSets.Rd
man/geneToSNPList.Rd
man/glossi.Rd
man/glossiMarginal.Rd
man/pValue-method.Rd
man/plotPvals.Rd
man/show-methods.Rd
man/simulate_chisq.Rd
man/simulatedStats-method.Rd
man/statistic-methods.Rd
man/vegas.Rd
man/vegasMarginal.Rd
tests
tests/runTests.R
vignettes
vignettes/cpvSNP.Rnw
cpvSNP documentation built on May 20, 2017, 9:45 p.m.

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