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 <email@example.com>|
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"'