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

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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
Date of publication
None
Maintainer
Caitlin McHugh <mchughc@uw.edu>
License
Artistic-2.0
Version
1.6.0

View on Bioconductor

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"'

Files in this package

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