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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cpvSNP")
AuthorCaitlin McHugh, Jessica Larson, and Jason Hackney
Bioconductor views GeneSetEnrichment Genetics GenomicVariation Pathways StatisticalMethod
Date of publicationNone
MaintainerCaitlin McHugh <mchughc@uw.edu>
LicenseArtistic-2.0
Version1.6.0

View on Bioconductor

Man pages

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"'

Functions

assocPvalBySetPlot Man page
createArrayData Man page
degreesOfFreedom Man page
degreesOfFreedom,GeneSetResultCollection-method Man page
degreesOfFreedom,GeneSetResult-method Man page
degreesOfFreedom,GLOSSIResultCollection-method Man page
degreesOfFreedom,GLOSSIResult-method Man page
degreesOfFreedom-methods Man page
degreesOfFreedom,VEGASResultCollection-method Man page
degreesOfFreedom,VEGASResult-method Man page
exampleArrayData Man page
geneSetAnalysis Man page
geneSetName Man page
geneSetName,GeneSetResultCollection-method Man page
geneSetName,GeneSetResult-method Man page
geneSetName,GLOSSIResultCollection-method Man page
geneSetName,GLOSSIResult-method Man page
geneSetName-methods Man page
geneSetName,VEGASResultCollection-method Man page
geneSetName,VEGASResult-method Man page
GeneSetResult-class Man page
GeneSetResultCollection-class Man page
geneSets Man page
geneToSNPList Man page
glossi Man page
glossiMarginal Man page
GLOSSIResult-class Man page
GLOSSIResultCollection-class Man page
plotPvals Man page
pValue Man page
pValue,GeneSetResultCollection-method Man page
pValue,GeneSetResult-method Man page
pValue,GLOSSIResultCollection-method Man page
pValue,GLOSSIResult-method Man page
pValue-methods Man page
pValue,VEGASResultCollection-method Man page
pValue,VEGASResult-method Man page
show Man page
show,GLOSSIResult-method Man page
show-methods Man page
show,VEGASResult-method Man page
simulate_chisq Man page
simulatedStats Man page
simulatedStats-methods Man page
simulatedStats,VEGASResultCollection-method Man page
simulatedStats,VEGASResult-method Man page
statistic Man page
statistic,GeneSetResultCollection-method Man page
statistic,GeneSetResult-method Man page
statistic,GLOSSIResultCollection-method Man page
statistic,GLOSSIResult-method Man page
statistic-methods Man page
statistic,VEGASResultCollection-method Man page
statistic,VEGASResult-method Man page
vegas Man page
vegasMarginal Man page
VEGASResult-class Man page
VEGASResultCollection-class Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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