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cpvSNP (version 1.0.0)

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

Description

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.

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Version

Version

1.0.0

License

Artistic-2.0

Maintainer

Caitlin McHugh

Last Published

February 15th, 2017

Functions in cpvSNP (1.0.0)

degreesOfFreedom-methods

~~ Methods for Function degreesOfFreedom ~~
pValue-methods

~~ Methods for Function pValue ~~
VEGASResult-class

Class "VEGASResult"
VEGASResultCollection-class

Class "VEGASResultCollection"
GLOSSIResultCollection-class

Class "GLOSSIResultCollection"
GLOSSIResult-class

Class "GLOSSIResult"
exampleArrayData

SNP Array Data to Use for Gene Set Analysis
plotPvals

Create a Plot of P-Values Against Number of SNPs per Set for All Sets in a Collection
geneSets

Gene Set Collection object
geneToSNPList

Translate a List of Gene Ids to Their Corresponding SNP Ids
geneSetAnalysis

Data to run gene set analysis methods
geneSetName-methods

~~ Methods for Function geneSetName ~~
summary-methods

~~ Methods for Function show in Package base ~~
vegas

Calculate the P-Value for a Set Using the VEGAS Method
simulate_chisq

Simulate a Chi-squared Statistic from a Distribution with a Specified Correlation Structure
vegasMarginal

Calculate the P-Value for a Set Using the VEGAS Method
assocPvalBySetPlot

Create a Density Plot of P-Values, Highlighting SNPs Within a Gene Set
glossiMarginal

Calculate a Chi-squared Statistic and P-Value for Items in a Set
glossi

Calculate a Chi-squared Statistic and P-Value for Independent Items of a Set Using the GLOSSI Method
createArrayData

Create a GRanges Object for a GWAS data.frame
GeneSetResult-class

Class "GeneSetResult"
GeneSetResultCollection-class

Class "GeneSetResultCollection"
simulatedStats-methods

~~ Methods for Function simulatedStats ~~
statistic-methods

~~ Methods for Function statistic ~~