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


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Documentation for package ‘cpvSNP’ version 1.32.0

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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"'