{ "_id": "6a1ad7081d7bb097a09e608d", "Package": "cpvSNP", "Type": "Package", "Title": "Gene set analysis methods for SNP association p-values that lie\nin genes in given gene sets", "Version": "1.45.0", "Date": "2021-11-20", "Author": "Caitlin McHugh, Jessica Larson, and Jason Hackney", "Maintainer": "Caitlin McHugh ", "Description": "Gene set analysis methods exist to combine SNP-level\nassociation p-values into gene sets, calculating a single\nassociation p-value for each gene set. This package implements\ntwo such methods that require only the calculated SNP p-values,\nthe gene set(s) of interest, and a correlation matrix (if\ndesired). One method (GLOSSI) requires independent SNPs and the\nother (VEGAS) can take into account correlation (LD) among the\nSNPs. Built-in plotting functions are available to help users\nvisualize results.", "License": "Artistic-2.0", "biocViews": "Genetics, StatisticalMethod, Pathways, GeneSetEnrichment,\nGenomicVariation", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:17 UTC", "RemoteUrl": "https://github.com/bioc/cpvSNP", "RemoteRef": "HEAD", "RemoteSha": "94067ad04b1aafb885f930b01952389f8805beea", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:49:33 UTC", "User": "root" }, "MD5sum": "a6dd26ae49a9df8147cd60e71eb9ec39", "_user": "bioc", "_type": "src", "_file": "cpvSNP_1.45.0.tar.gz", "_fileid": "37c6165ddca824d990aacb18d517d5c77b983ad30a25df96fc278901ee40e5ff", "_filesize": 2254519, "_sha256": "37c6165ddca824d990aacb18d517d5c77b983ad30a25df96fc278901ee40e5ff", "_created": "2026-05-30T08:49:33.000Z", "_published": "2026-05-30T12:24:40.828Z", "_jobs": [ 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"Create a Density Plot of P-Values, Highlighting SNPs Within a Gene Set", "topics": [ "assocPvalBySetPlot" ] }, { "page": "createArrayData", "title": "Create a GRanges Object for a GWAS data.frame", "topics": [ "createArrayData" ] }, { "page": "degreesOfFreedom-method", "title": "~~ Methods for Function 'degreesOfFreedom' ~~", "topics": [ "degreesOfFreedom", "degreesOfFreedom,GeneSetResult-method", "degreesOfFreedom,GeneSetResultCollection-method", "degreesOfFreedom,GLOSSIResult-method", "degreesOfFreedom,GLOSSIResultCollection-method", "degreesOfFreedom,VEGASResult-method", "degreesOfFreedom,VEGASResultCollection-method", "degreesOfFreedom-methods" ] }, { "page": "exampleArrayData", "title": "SNP Array Data to Use for Gene Set Analysis", "topics": [ "exampleArrayData" ] }, { "page": "geneSetAnalysis", "title": "Data to run gene set analysis methods", "topics": [ "geneSetAnalysis" ] }, { "page": "geneSetName-methods", "title": "~~ Methods for Function 'geneSetName' ~~", "topics": [ "geneSetName", "geneSetName,GeneSetResult-method", "geneSetName,GeneSetResultCollection-method", "geneSetName,GLOSSIResult-method", "geneSetName,GLOSSIResultCollection-method", "geneSetName,VEGASResult-method", "geneSetName,VEGASResultCollection-method", "geneSetName-methods" ] }, { "page": "GeneSetResult-class", "title": "Class '\"GeneSetResult\"'", "topics": [ "GeneSetResult-class" ] }, { "page": "GeneSetResultCollection-class", "title": "Class '\"GeneSetResultCollection\"'", "topics": [ "GeneSetResultCollection-class" ] }, { "page": "geneSets", "title": "Gene Set Collection object", "topics": [ "geneSets" ] }, { "page": "geneToSNPList", "title": "Translate a List of Gene Ids to Their Corresponding SNP Ids", "topics": [ "geneToSNPList" ] }, { "page": "glossi", "title": "Calculate a Chi-squared Statistic and P-Value for Independent Items of a Set Using the GLOSSI Method", "topics": [ "glossi" ] }, { "page": "glossiMarginal", "title": "Calculate a Chi-squared Statistic and P-Value for Items in a Set", "topics": [ "glossiMarginal" ] }, { "page": "GLOSSIResult-class", "title": "Class '\"GLOSSIResult\"'", "topics": [ "GLOSSIResult-class" ] }, { "page": "GLOSSIResultCollection-class", "title": "Class '\"GLOSSIResultCollection\"'", "topics": [ "GLOSSIResultCollection-class" ] }, { "page": "plotPvals", "title": "Create a Plot of P-Values Against Number of SNPs per Set for All Sets in a Collection", "topics": [ "plotPvals" ] }, { "page": "pValue-method", "title": "~~ Methods for Function 'pValue' ~~", "topics": [ "pValue", "pValue,GeneSetResult-method", "pValue,GeneSetResultCollection-method", "pValue,GLOSSIResult-method", "pValue,GLOSSIResultCollection-method", "pValue,VEGASResult-method", "pValue,VEGASResultCollection-method", "pValue-methods" ] }, { "page": "simulate_chisq", "title": "Simulate a Chi-squared Statistic from a Distribution with a Specified Correlation Structure", "topics": [ "simulate_chisq" ] }, { "page": "simulatedStats-method", "title": "~~ Methods for Function 'simulatedStats' ~~", "topics": [ "simulatedStats", "simulatedStats,VEGASResult-method", "simulatedStats,VEGASResultCollection-method", "simulatedStats-methods" ] }, { "page": "statistic-methods", "title": "~~ Methods for Function 'statistic' ~~", "topics": [ "statistic", "statistic,GeneSetResult-method", "statistic,GeneSetResultCollection-method", "statistic,GLOSSIResult-method", "statistic,GLOSSIResultCollection-method", "statistic,VEGASResult-method", "statistic,VEGASResultCollection-method", "statistic-methods" ] }, { "page": "show-methods", "title": "~~ Methods for Function 'show' in Package 'base' ~~", "topics": [ "show", "show,GLOSSIResult-method", "show,VEGASResult-method", "show-methods" ] }, { "page": "vegas", "title": "Calculate the P-Value for a Set Using the VEGAS Method", "topics": [ "vegas" ] }, { "page": "vegasMarginal", "title": "Calculate the P-Value for a Set Using the VEGAS Method", "topics": [ "vegasMarginal" ] }, { "page": "VEGASResult-class", "title": 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