{ "_id": "6a4b4e27a6574ff277f994dd", "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": "2026-07-06 06:32:19 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "cpvSNP_1.45.0.tar.gz", "_fileid": "https://r2.ropensci.org/0317eb135437c8823df15bda16d43b2dba769c805201eda74f1d48c88102639f", "_filesize": 2255517, "_sha256": "0317eb135437c8823df15bda16d43b2dba769c805201eda74f1d48c88102639f", "_expires": "2026-10-14T06:41:41.000Z", "_created": "2026-07-06T06:32:19.000Z", "_published": "2026-07-06T06:41:43.117Z", "_bioccheck": { "error": 2, "warning": 7, "note": 14 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28772294555", "_status": "success", "_upstream": "https://github.com/bioc/cpvSNP", "_commit": { "id": "94067ad04b1aafb885f930b01952389f8805beea", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380017 }, "_maintainer": { "name": "Caitlin McHugh", "email": "mchughc@uw.edu", "login": "mchughc", "description": "", "uuid": 6343156 }, "_distro": "resolute", "_jobs": [ { "job": 85309223974, "time": 276, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8101414560" }, { "job": 85309223980, "time": 448, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8101465169" }, { "job": 85309223972, "time": 491, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": 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"role": "Depends" }, { "package": "GSEABase", "version": ">= 1.24.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "corpcor", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "ReportingTools", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23" } ], "_topics": [ "genetics", "statisticalmethod", "pathways", "genesetenrichment", "genomicvariation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 5, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/cpvSNP.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "assocPvalBySetPlot", "createArrayData", "degreesOfFreedom", "geneSetName", "geneToSNPList", "glossi", "glossiMarginal", "plotPvals", "pValue", "simulate_chisq", "simulatedStats", "statistic", "vegas", "vegasMarginal" ], "_datasets": [ { "name": "geneSetAnalysis", "title": "Data to run gene set analysis methods", "object": "geneSetAnalysis", "file": "geneSetAnalysis.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "assocPvalBySetPlot", "title": "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": "Class 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