{ "_id": "6a1d27641d7bb097a0a38204", "Package": "SNPRelate", "Type": "Package", "Title": "Parallel Computing Toolset for Relatedness and Principal\nComponent Analysis of SNP Data", "Version": "1.47.0", "Date": "2026-04-13", "Authors@R": "c(person(\"Xiuwen\", \"Zheng\", role=c(\"aut\", \"cre\", \"cph\"),\nemail=\"zhengx@u.washington.edu\", comment=c(ORCID=\"0000-0002-1390-0708\")),\nperson(\"Stephanie\", \"Gogarten\", role=\"ctb\", email=\"sdmorris@uw.edu\"),\nperson(\"Cathy\", \"Laurie\", role=\"ctb\", email=\"cclaurie@uw.edu\"),\nperson(\"Bruce\", \"Weir\", role=c(\"ctb\", \"ths\"), email=\"bsweir@uw.edu\",\ncomment=c(ORCID=\"0000-0002-4883-1247\")))", "Description": "Genome-wide association studies (GWAS) are widely used to\ninvestigate the genetic basis of diseases and traits, but they\npose many computational challenges. We developed an R package\nSNPRelate to provide a binary format for single-nucleotide\npolymorphism (SNP) data in GWAS utilizing CoreArray Genomic\nData Structure (GDS) data files. The GDS format offers the\nefficient operations specifically designed for integers with\ntwo bits, since a SNP could occupy only two bits. SNPRelate is\nalso designed to accelerate two key computations on SNP data\nusing parallel computing for multi-core symmetric\nmultiprocessing computer architectures: Principal Component\nAnalysis (PCA) and relatedness analysis using\nIdentity-By-Descent measures. The SNP GDS format is also used\nby the GWASTools package with the support of S4 classes and\ngeneric functions. The extended GDS format is implemented in\nthe SeqArray package to support the storage of single\nnucleotide variations (SNVs), insertion/deletion polymorphism\n(indel) and structural variation calls in whole-genome and\nwhole-exome variant data.", "License": "GPL-3", "VignetteBuilder": "knitr", "LazyData": "true", "URL": "https://github.com/zhengxwen/SNPRelate", "BugReports": "https://github.com/zhengxwen/SNPRelate/issues", "biocViews": "Infrastructure, Genetics, StatisticalMethod,\nPrincipalComponent", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:39:41 UTC", "RemoteUrl": "https://github.com/bioc/SNPRelate", "RemoteRef": "HEAD", "RemoteSha": "9dd380bbcbc3385aa9ab56a91b33302c0480b2c5", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 09:32:53 UTC", "User": "root" }, "Author": "Xiuwen Zheng [aut, cre, cph] (ORCID:\n),\nStephanie Gogarten [ctb],\nCathy Laurie [ctb],\nBruce Weir [ctb, ths] (ORCID: )", "Maintainer": "Xiuwen Zheng ", "MD5sum": 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"_homeurl": "https://github.com/zhengxwen/snprelate", "_realowner": "bioc", "_cranurl": false, "_releases": [ { "version": "0.9.0", "date": "2011-08-03" }, { "version": "0.9.1", "date": "2011-08-13" }, { "version": "0.9.2", "date": "2012-02-02" }, { "version": "0.9.3", "date": "2012-03-05" }, { "version": "0.9.4", "date": "2012-03-17" }, { "version": "0.9.5", "date": "2012-04-25" }, { "version": "0.9.6", "date": "2012-07-22" }, { "version": "0.9.7", "date": "2012-08-30" }, { "version": "0.9.8", "date": "2012-09-29" }, { "version": "0.9.9", "date": "2013-01-05" }, { "version": "0.9.10", "date": "2013-01-21" }, { "version": "0.9.11", "date": "2013-01-31" }, { "version": "0.9.12", "date": "2013-02-19" }, { "version": "0.9.13", "date": "2013-02-26" }, { "version": "0.9.14", "date": "2013-05-22" }, { "version": "0.9.15", "date": "2013-06-09" }, { "version": "0.9.16", "date": "2013-08-20" }, { "version": "0.9.17", "date": "2013-09-05" }, { "version": "0.9.18", "date": "2013-09-29" }, { 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"snpgdsSelectSNP", "snpgdsSlidingWindow", "snpgdsSNPList", "snpgdsSNPListIntersect", "snpgdsSNPRateFreq", "snpgdsSummary", "snpgdsTranspose", "snpgdsVCF2GDS", "snpgdsVCF2GDS_R" ], "_datasets": [ { "name": "hapmap_geno", "title": "SNP genotypes of HapMap samples", "object": "hapmap_geno", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "SNPRelate-package", "title": "Parallel Computing Toolset for Genome-Wide Association Studies", "topics": [ "SNPRelate-package", "SNPRelate" ] }, { "page": "hapmap_geno", "title": "SNP genotypes of HapMap samples", "topics": [ "hapmap_geno" ] }, { "page": "snpgdsAdmixPlot", "title": "Plot Ancestry Proportions", "topics": [ "snpgdsAdmixPlot", "snpgdsAdmixTable" ] }, { "page": "snpgdsAdmixProp", "title": "Estimate ancestral proportions from the eigen-analysis", "topics": [ "snpgdsAdmixProp" ] }, { "page": "snpgdsAlleleSwitch", "title": "Allele-switching", "topics": [ "snpgdsAlleleSwitch" ] }, { "page": "snpgdsApartSelection", "title": "Select SNPs with a basepair distance", "topics": [ "snpgdsApartSelection" ] }, { "page": "snpgdsBED2GDS", "title": "Conversion from PLINK BED to GDS", "topics": [ "snpgdsBED2GDS" ] }, { "page": "snpgdsClose", "title": "Close the SNP GDS File", "topics": [ "snpgdsClose" ] }, { "page": "snpgdsCombineGeno", "title": "Merge SNP datasets", "topics": [ "snpgdsCombineGeno" ] }, { "page": "snpgdsCreateGeno", "title": "Create a SNP genotype dataset from a matrix", "topics": [ "snpgdsCreateGeno" ] }, { "page": "snpgdsCreateGenoSet", "title": "Create a SNP genotype dataset from a GDS file", "topics": [ "snpgdsCreateGenoSet" ] }, { "page": "snpgdsCutTree", "title": "Determine clusters of individuals", "topics": [ "snpgdsCutTree" ] }, { "page": "snpgdsDiss", "title": "Individual dissimilarity analysis", "topics": [ "snpgdsDiss" ] }, { "page": "snpgdsDrawTree", "title": "Draw a dendrogram", "topics": [ "snpgdsDrawTree" ] }, { "page": "snpgdsEIGMIX", "title": "Eigen-analysis on SNP genotype data", "topics": [ "plot.snpgdsEigMixClass", "snpgdsEIGMIX" ] }, { "page": "snpgdsErrMsg", "title": "Get the last error information", "topics": [ "snpgdsErrMsg" ] }, { "page": "snpgdsExampleFileName", "title": "Example GDS file", "topics": [ "snpgdsExampleFileName" ] }, { "page": "SNPGDSFileClass-class", "title": "SNPGDSFileClass", "topics": [ "SNPGDSFileClass", "SNPGDSFileClass-class" ] }, { "page": "snpgdsFst", "title": "F-statistics (fixation indices)", "topics": [ "snpgdsFst" ] }, { "page": "snpgdsGDS2BED", "title": "Conversion from GDS to PLINK BED", "topics": [ "snpgdsGDS2BED" ] }, { "page": "snpgdsGDS2Eigen", "title": "Conversion from GDS to Eigen (EIGENSTRAT)", "topics": [ "snpgdsGDS2Eigen" ] }, { "page": "snpgdsGDS2PED", "title": "Conversion from GDS to PED", "topics": [ "snpgdsGDS2PED" ] }, { "page": "snpgdsGEN2GDS", "title": "Conversion from Oxford GEN format to GDS", "topics": [ "snpgdsGEN2GDS" ] }, { "page": "snpgdsGetGeno", "title": "To get a genotype matrix", "topics": [ "snpgdsGetGeno" ] }, { "page": "snpgdsGRM", "title": "Genetic Relationship Matrix (GRM) for SNP genotype data", "topics": [ "snpgdsGRM" ] }, { "page": "snpgdsHCluster", "title": "Hierarchical cluster analysis", "topics": [ "snpgdsHCluster" ] }, { "page": "snpgdsHWE", "title": "Statistical test of Hardy-Weinberg Equilibrium", "topics": [ "snpgdsHWE" ] }, { "page": "snpgdsIBDKING", "title": "KING method of moment for the identity-by-descent (IBD) analysis", "topics": [ "snpgdsIBDKING" ] }, { "page": "snpgdsIBDMLE", "title": "Maximum likelihood estimation (MLE) for the Identity-By-Descent (IBD) Analysis", "topics": [ "snpgdsIBDMLE" ] }, { "page": "snpgdsIBDMLELogLik", "title": "Log likelihood for MLE method in the Identity-By-Descent (IBD) Analysis", "topics": [ "snpgdsIBDMLELogLik" ] }, { "page": "snpgdsIBDMoM", "title": "PLINK method of moment (MoM) for the Identity-By-Descent (IBD) Analysis", "topics": [ "snpgdsIBDMoM" ] }, { "page": "snpgdsIBDSelection", "title": "Get a table of IBD coefficients", "topics": [ "snpgdsIBDSelection" ] }, { "page": "snpgdsIBS", "title": "Identity-By-State (IBS) proportion", "topics": [ "snpgdsIBS" ] }, { "page": "snpgdsIBSNum", "title": "Identity-By-State (IBS)", "topics": [ "snpgdsIBSNum" ] }, { "page": "snpgdsIndInb", "title": "Individual Inbreeding Coefficients", "topics": [ "snpgdsIndInb" ] }, { "page": "snpgdsIndInbCoef", "title": "Individual Inbreeding Coefficient", "topics": [ "snpgdsIndInbCoef" ] }, { "page": "snpgdsIndivBeta", "title": "Individual inbreeding and relatedness estimation (beta estimator)", "topics": [ "snpgdsIndivBeta", "snpgdsIndivBetaRel" ] }, { "page": "snpgdsLDMat", "title": "Linkage Disequilibrium (LD) analysis", "topics": [ "snpgdsLDMat" ] }, { "page": "snpgdsLDpair", "title": "Linkage Disequilibrium (LD)", "topics": [ "snpgdsLDpair" ] }, { "page": "snpgdsLDpruning", "title": "Linkage Disequilibrium (LD) based SNP pruning", "topics": [ "snpgdsLDpruning" ] }, { "page": "snpgdsMergeGRM", "title": "Merge Multiple Genetic Relationship Matrices (GRM)", "topics": [ "snpgdsMergeGRM" ] }, { "page": "snpgdsOpen", "title": "Open a SNP GDS File", "topics": [ "snpgdsOpen" ] }, { "page": "snpgdsOption", "title": "Option settings: chromosome coding, etc", "topics": [ "snpgdsOption" ] }, { "page": "snpgdsPairIBD", "title": "Calculate Identity-By-Descent (IBD) Coefficients", "topics": [ "snpgdsPairIBD" ] }, { "page": "snpgdsPairIBDMLELogLik", "title": "Log likelihood for MLE method in the Identity-By-Descent (IBD) Analysis", "topics": [ "snpgdsPairIBDMLELogLik" ] }, { "page": "snpgdsPairScore", "title": "Genotype Score for Pairs of Individuals", "topics": [ "snpgdsPairScore" ] }, { "page": "snpgdsPCA", "title": "Principal Component Analysis (PCA) on SNP genotype data", "topics": [ "plot.snpgdsPCAClass", "snpgdsPCA" ] }, { "page": "snpgdsPCACorr", "title": "PC-correlated SNPs in principal component analysis", "topics": [ "snpgdsPCACorr" ] }, { "page": "snpgdsPCASampLoading", "title": "Project individuals onto existing principal component axes", "topics": [ "snpgdsPCASampLoading" ] }, { "page": "snpgdsPCASNPLoading", "title": "SNP loadings in principal component analysis", "topics": [ "snpgdsPCASNPLoading" ] }, { "page": "snpgdsPED2GDS", "title": "Conversion from PLINK PED to GDS", "topics": [ "snpgdsPED2GDS" ] }, { "page": "snpgdsSampMissRate", "title": "Missing Rate of Samples", "topics": [ "snpgdsSampMissRate" ] }, { "page": "snpgdsSelectSNP", "title": "SNP selection", "topics": [ "snpgdsSelectSNP" ] }, { "page": "snpgdsSlidingWindow", "title": "Sliding window", "topics": [ "snpgdsSlidingWindow" ] }, { "page": "snpgdsSNPList", "title": "Create a SNP list object", "topics": [ "snpgdsSNPList" ] }, { "page": "snpgdsSNPListClass", "title": "the class of a SNP list", "topics": [ "snpgdsSNPListClass" ] }, { "page": "snpgdsSNPListIntersect", "title": "Get a common SNP list between/among SNP list objects", "topics": [ "snpgdsSNPListIntersect" ] }, { "page": "snpgdsSNPRateFreq", "title": "Allele Frequency, Minor Allele Frequency, Missing Rate of SNPs", "topics": [ "snpgdsSNPRateFreq" ] }, { "page": "snpgdsSummary", "title": "Summary of GDS genotype file", "topics": [ "snpgdsSummary" ] }, { "page": "snpgdsTranspose", "title": "Transpose genotypic matrix", "topics": [ "snpgdsTranspose" ] }, { "page": "snpgdsVCF2GDS", "title": "Reformat VCF file(s)", "topics": [ "snpgdsVCF2GDS" ] }, { "page": "snpgdsVCF2GDS_R", "title": "Reformat a VCF file (R implementation)", "topics": [ "snpgdsVCF2GDS_R" ] } ], "_readme": "https://github.com/bioc/SNPRelate/raw/HEAD/README.md", "_rundeps": [ "gdsfmt", "RhpcBLASctl" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", 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Likelihood Estimation (MLE)", "Relationship inference Using KING method of moments", "Identity-By-State Analysis", "Integration with SeqArray", "Function List", "Resources", "Session Information", "References", "Acknowledgements" ], "created": "2019-10-14 19:11:01", "modified": "2022-07-15 05:44:16", "commits": 7 } ], "_score": 12.695637101443005, "_indexed": true, "_nocasepkg": "snprelate", "_universes": [ "bioc", "zhengxwen" ], "_binaries": [ { "r": "4.7.0", "os": "win", "version": "1.45.1", "date": "2026-04-14T06:35:44.000Z", "arch": "x86_64", "commit": "5a8a64ef4c665e3c595696814c6767d9adac5172", "fileid": "9a45b655707c3313f2456c85d10dce9533c51f89e74c1fb89e306deabbf50c49", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/24384532702" }, { "r": "4.5.3", "os": "win", "version": "1.45.1", "date": "2026-04-14T06:35:14.000Z", "arch": "x86_64", "commit": "5a8a64ef4c665e3c595696814c6767d9adac5172", "fileid": 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