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

## Documentation for package ‘cpvSNP’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

assocPvalBySetPlot | Create a Density Plot of P-Values, Highlighting SNPs Within a Gene Set
createArrayData | Create a GRanges Object for a GWAS data.frame
degreesOfFreedom | ~~ Methods for Function 'degreesOfFreedom' ~~
degreesOfFreedom-method | ~~ Methods for Function 'degreesOfFreedom' ~~
degreesOfFreedom-methods | ~~ Methods for Function 'degreesOfFreedom' ~~
exampleArrayData | SNP Array Data to Use for Gene Set Analysis
geneSetAnalysis | Data to run gene set analysis methods
geneSetName | ~~ Methods for Function 'geneSetName' ~~
geneSetName-method | ~~ Methods for Function 'geneSetName' ~~
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 Items of a Set Using the GLOSSI Method
glossiMarginal | Calculate a Chi-squared Statistic and P-Value for Items in a Set
GLOSSIResult-class | Class '"GLOSSIResult"'
GLOSSIResultCollection-class | Class '"GLOSSIResultCollection"'
plotPvals | Create a Plot of P-Values Against Number of SNPs per Set for All Sets in a Collection
pValue | ~~ Methods for Function 'pValue' ~~
pValue-method | ~~ Methods for Function 'pValue' ~~
pValue-methods | ~~ Methods for Function 'pValue' ~~
show | ~~ Methods for Function 'show' in Package 'base' ~~
show-method | ~~ Methods for Function 'show' in Package 'base' ~~
show-methods | ~~ Methods for Function 'show' in Package 'base' ~~
simulatedStats | ~~ Methods for Function 'simulatedStats' ~~
simulatedStats-method | ~~ Methods for Function 'simulatedStats' ~~
simulatedStats-methods | ~~ Methods for Function 'simulatedStats' ~~
simulate_chisq | Simulate a Chi-squared Statistic from a Distribution with a Specified Correlation Structure
statistic | ~~ Methods for Function 'statistic' ~~
statistic-method | ~~ Methods for Function 'statistic' ~~
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"'