Gene set analysis methods for SNP association p-values that lie
in genes in given gene sets
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘cpvSNP’ version 1.32.0
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"' |