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 |

**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"'

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

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