{ "_id": "6a2a95ba7b7a29ca6004ea38", "Encoding": "UTF-8", "Package": "hJAM", "Type": "Package", "Title": "Hierarchical Joint Analysis of Marginal Summary Statistics", "Version": "1.0.0", "Author": "Lai Jiang ", "Maintainer": "Lai Jiang ", "Description": "Provides functions to implement a hierarchical approach\nwhich is designed to perform joint analysis of summary\nstatistics using the framework of Mendelian Randomization or\ntranscriptome analysis. Reference: Lai Jiang, Shujing Xu,\nNicholas Mancuso, Paul J. Newcombe, David V. Conti (2020). \"A\nHierarchical Approach Using Marginal Summary Statistics for\nMultiple Intermediates in a Mendelian Randomization or\nTranscriptome Analysis.\"\n.", "License": "MIT + file LICENSE", "LazyData": "true", "RoxygenNote": "6.1.1", "VignetteBuilder": "knitr", "URL": "https://github.com/lailylajiang/hJAM", "BugReports": "https://github.com/lailylajiang/hJAM/issues", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-11 10:26:50 UTC", "User": "root" }, "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://cranhaven.r-universe.dev", "Date/Publication": "2026-06-11 01:02:00 UTC", "RemoteUrl": "https://github.com/cranhaven/cranhaven.r-universe.dev", "RemoteRef": "package/hJAM", "RemoteSha": "11b59d5682341b18ebec9da6fc21ee554d7927db", "RemoteSubdir": "hJAM", "MD5sum": "968cb13441618024a6082272cc149b9f", "_user": "cranhaven", "_type": "src", "_file": "hJAM_1.0.0.tar.gz", "_fileid": "cc77d0f4f20387061c2e15552badd6286b1fabac78e3299a8a8f5ddc201d9b8e", "_filesize": 790663, "_sha256": "cc77d0f4f20387061c2e15552badd6286b1fabac78e3299a8a8f5ddc201d9b8e", "_created": "2026-06-11T10:26:50.000Z", "_published": "2026-06-11T11:02:18.221Z", "_distro": "noble", "_jobs": [ { "job": 80775708297, "time": 212, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7561594176" }, { "job": 80775708333, "time": 144, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7561571094" }, { "job": 80775708235, "time": 101, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7562266689" }, { "job": 80775708265, "time": 114, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7562229063" }, { "job": 80775112321, "time": 204, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7561519878" }, { "job": 80775708287, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7561559015" }, { "job": 80775708284, "time": 121, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7561562075" }, { "job": 80775708393, "time": 113, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7561560002" }, { "job": 80775708271, "time": 108, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7561557809" } ], "_buildurl": "https://github.com/r-universe/cranhaven/actions/runs/27340273363", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cranhaven/cranhaven.r-universe.dev", "_commit": { "id": "11b59d5682341b18ebec9da6fc21ee554d7927db", "author": "GitHub Action ", "committer": "GitHub Action ", "message": "Add hJAM to CRANhaven, because archived on 2026-06-11 01:02:00 +0000\n", "time": 1781139720 }, "_maintainer": { "name": "Lai Jiang", "email": "jian848@usc.edu", "login": "lailylajiang", "description": "Biostatistics PhD", "uuid": 43098508 }, "_registered": true, "_dependencies": [ { "package": "ggplot2", "role": "Imports" }, { "package": "ggpubr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cranhaven", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-24", "n": 1 } ], "_tags": [], "_topics": [ "archived", "packages", "r-universe" ], "_stars": 5, "_contributors": [ { "user": "henrikbengtsson", "count": 183, "uuid": 1616850 } ], "_userbio": { "uuid": 161993010, "type": "organization", "name": "cranhaven", "description": "CRANhaven - Repository for Recently Archived CRAN Packages" }, "_downloads": { "count": 185, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hJAM" }, "_devurl": "https://github.com/lailylajiang/hjam", "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hJAM.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/uscbiostats/hjam", "_realowner": "uscbiostats", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2020-02-20" } ], "_exports": [ "get_cond_A", "get_cond_alpha", "hJAM_egger", "hJAM_lnreg", "output.format", "SNPs_heatmap", "SNPs_scatter_plot" ], "_datasets": [ { "name": "betas.Gy", "title": "Example beta list of hJAM", "object": "betas.Gy", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "conditional_A", "title": "Example conditional A matrix of hJAM", "object": "conditional_A", "class": [ "matrix", "array" ], "fields": [ "bmi", "t2d" ], "rows": 210, "table": true, "tojson": true }, { "name": "Gl", "title": "Example reference data of hJAM", "object": "Gl", "class": [ "data.frame" ], "fields": [ "rs2296173_G", "rs657452_A", "rs12088739_A", "rs3101336_C", "rs12566985_G", "rs12401738_A", "rs11165643_T", "rs17024393_C", "rs1127655_C", "rs2493394_G", "rs543874_G", "rs2820292_C", "rs340874_C", "rs2820426_G", "rs348330_G", "rs2867125_C", "rs13021737_G", "rs10182181_G", "rs11126666_A", "rs780094_C", "rs17334919_C", "rs1016287_T", "rs243019_C", "rs11688816_G", "rs1009358_T", "rs10169613_C", "rs12617659_C", "rs2121279_T", "rs7572970_G", "rs13389219_C", "rs1528435_T", "rs7599312_G", "rs2972144_G", "rs7561798_G", "rs1899951_C", "rs1496653_A", "rs6804842_G", "rs11926707_C", "rs2365389_C", "rs2292662_C", "rs6795735_C", "rs3849570_A", "rs13078960_G", "rs11708067_A", "rs16851483_T", "rs9844972_C", "rs4472028_T", "rs11925227_G", "rs7651090_G", "rs1516725_C", "rs3887925_T", "rs6808574_C", "rs1801214_T", "rs10938397_G", "rs17086692_G", "rs17001654_G", "rs993380_A", "rs13107325_T", "rs7674212_G", "rs11098676_C", "rs11727676_T", "rs7685296_C", "rs735949_T", "rs1061813_G", "rs4865796_A", "rs459193_G", "rs3900856_A", "rs2307111_T", "rs2112347_T", "rs6878122_G", "rs7729395_T", "rs10077431_C", "rs1050226_A", "rs7756992_G", "rs2857605_T", "rs2071479_T", "rs205262_G", "rs2033529_G", "rs9369425_G", "rs72892910_T", "rs2207139_G", "rs9400239_C", "rs853974_T", "rs2246012_C", "rs622217_T", "rs13191362_A", "rs17168486_T", "rs2191348_T", "rs849135_G", "rs2908282_A", "rs1167827_G", "rs2245368_C", "rs2299383_T", "rs13239186_T", "rs13234269_T", "rs7786095_A", "rs7841082_T", "rs17411031_C", "rs10087241_G", "rs12681990_C", "rs516946_C", "rs17405819_T", "rs2033732_C", "rs7845219_T", "rs3802177_G", "rs2294120_A", "rs10974438_C", "rs4740619_T", "rs1063192_A", "rs10811661_T", "rs10968576_G", "rs1758632_G", "rs17791483_A", "rs2796441_G", "rs10114341_T", "rs6477694_C", "rs1928295_T", "rs10733682_A", "rs687621_G", "rs11257655_T", "rs2616132_A", "rs2633310_G", "rs753270_C", "rs7899106_G", "rs7923866_C", "rs11591741_G", "rs17094222_C", "rs11191560_C", "rs7903146_T", "rs4918796_C", "rs2421016_C", "rs2237892_C", "rs4256980_G", "rs5215_C", "rs11030104_A", "rs2176598_T", "rs3817334_T", "rs7929543_C", "rs1552224_A", "rs10830963_G", "rs12286929_G", "rs7931302_C", "rs67232546_T", "rs12299509_G", "rs11048456_C", "rs10842994_C", "rs7138803_A", "rs2261181_T", "rs1480474_G", "rs7138300_C", "rs11107116_T", "rs61953351_G", "rs11057405_G", "rs940904_A", "rs825476_T", "rs9581854_T", "rs576674_G", "rs963740_A", "rs12429545_A", "rs1359790_G", "rs10132280_C", "rs12885454_C", "rs11847697_T", "rs7141420_T", "rs7144011_T", "rs3736485_A", "rs4502156_T", "rs982077_A", "rs16951275_T", "rs7177055_A", "rs4932143_G", "rs12910825_G", "rs9940149_G", "rs758747_T", "rs12446632_G", "rs2650492_A", "rs9925964_A", "rs1558902_A", "rs7185735_G", "rs244415_G", "rs77258096_C", "rs2925979_T", "rs8068804_A", "rs1000940_G", "rs12945601_T", "rs11651755_C", "rs17405722_A", "rs9911983_T", "rs9894220_A", "rs302864_A", "rs17631783_C", "rs12940622_G", "rs7240767_C", "rs1808579_C", "rs7243357_T", "rs6567160_C", "rs12970134_A", "rs17724992_A", "rs10401969_C", "rs29941_G", "rs2075650_A", "rs8108269_G", "rs2287019_C", "rs3810291_A", "rs6515236_A", "rs6059662_G", "rs4810426_T", "rs6066138_G", "rs16988333_A", "rs4823182_G" ], "rows": 2467, "table": true, "tojson": true }, { "name": "marginal_A", "title": "Example marginal A matrix of hJAM", "object": "marginal_A", "class": [ "matrix", "array" ], "fields": [ "bmi", "t2d" ], "rows": 210, "table": true, "tojson": true }, { "name": "SNPs_info", "title": "Example SNPs' information of hJAM", "object": "SNPs_info", "class": [ "data.frame" ], "fields": [ "SNP", "Major_A", "ref_frq" ], "rows": 210, "table": true, "tojson": true } ], "_help": [ { "page": "betas.Gy", "title": "Example beta list of hJAM", "topics": [ "betas.Gy" ] }, { "page": "conditional_A", "title": "Example conditional A matrix of hJAM", "topics": [ "conditional_A" ] }, { "page": "get_cond_A", "title": "Compute conditional Z matrix", "topics": [ "get_cond_A" ] }, { "page": "get_cond_alpha", "title": "Compute conditional alphas", "topics": [ "get_cond_alpha" ] }, { "page": "Gl", "title": "Example reference data of hJAM", "topics": [ "Gl" ] }, { "page": "hJAM_egger", "title": "Fit hJAM with Egger regression", "topics": [ "hJAM_egger" ] }, { "page": "hJAM_lnreg", "title": "Fit hJAM with linear regression", "topics": [ "hJAM_lnreg" ] }, { "page": "marginal_A", "title": "Example marginal A matrix of hJAM", "topics": [ "marginal_A" ] }, { "page": "output.format", "title": "Keep the output as three digits", "topics": [ "output.format" ] }, { "page": "print.hJAM_egger", "title": "Print out for hJAM_egger", "topics": [ "print.hJAM_egger" ] }, { "page": "print.hJAM_lnreg", "title": "Print out for hJAM_lnreg", "topics": [ "print.hJAM_lnreg" ] }, { "page": "SNPs_heatmap", "title": "Heatmap for all the SNPs used in the analysis", "topics": [ "SNPs_heatmap" ] }, { "page": "SNPs_info", "title": "Example SNPs' information of hJAM", "topics": [ "SNPs_info" ] }, { "page": "SNPs_scatter_plot", "title": "Scatter plot for all the SNPs used in the analysis", "topics": [ "SNPs_scatter_plot" ] } ], "_readme": "https://github.com/cranhaven/cranhaven.r-universe.dev/raw/package/hJAM/hJAM/README.md", "_rundeps": [ "abind", "backports", "boot", "broom", "car", "carData", "cli", "colorspace", "corrplot", "cowplot", "cpp11", "Deriv", "doBy", "dplyr", "farver", "forecast", "Formula", "fracdiff", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "mgcv", "microbenchmark", "minqa", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "pbkrtest", "pillar", "pkgconfig", "plyr", "polynom", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "reshape2", "rlang", "rstatix", "S7", "scales", "SparseM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "hJAM_vignette.Rmd", "filename": "hJAM_vignette.html", "title": "hJAM Vignette", "author": "Lai Jiang", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Implementation", "General input", "Get conditional $\\hat{A}$ matrix", "Example", "Data exploration", "Conversion of $\\hat{A}$ matrix", "hJAM", "Conclusion" ], "created": "2026-06-11 01:02:00", "modified": "2026-06-11 01:02:00", "commits": 1 } ], "_score": 3.3979400086720375, "_indexed": false, "_nocasepkg": "hjam", "_universes": [ "cranhaven" ], "_indexurl": "https://uscbiostats.r-universe.dev/hJAM", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-06-11T10:30:01.000Z", "distro": "noble", "commit": "11b59d5682341b18ebec9da6fc21ee554d7927db", "fileid": "fedbcab2f690d8172e48ccbeec91be44dff0f051777c53310a713a62c8acfb8f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/27340273363" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-06-11T10:29:01.000Z", "distro": "noble", "commit": "11b59d5682341b18ebec9da6fc21ee554d7927db", "fileid": "43bfdfcdf63beaf3b570aa936821cf7a6e5c71f844d71fe423c2cab60fca7e5b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/27340273363" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-06-11T11:01:43.000Z", "commit": "11b59d5682341b18ebec9da6fc21ee554d7927db", "fileid": "d1d230801fbeade508bae45d9c8f361ec756c315dfb0bd22e0d5cc88d9828015", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/27340273363" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-06-11T10:59:54.000Z", "commit": "11b59d5682341b18ebec9da6fc21ee554d7927db", "fileid": "e2244f2144cc41cb4621317a05dbd93db6bfcd6c08df5f8146ec2b628b99379c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/27340273363" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-06-11T10:28:55.000Z", "commit": "11b59d5682341b18ebec9da6fc21ee554d7927db", "fileid": "acdb6a1efe26b294d79d7c07e65cff0b08613e085a64608978ccf6c9fa310d2f", "status": "success", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/27340273363" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-06-11T10:28:23.000Z", "commit": "11b59d5682341b18ebec9da6fc21ee554d7927db", "fileid": "e5dbf0c8b88540bf58dde0fe886be3041d965a1bf4607eedc0bdd2b271d1203a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/27340273363" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-06-11T10:28:14.000Z", "commit": "11b59d5682341b18ebec9da6fc21ee554d7927db", "fileid": "349e61b34d7985f7ee1fffe979d74f57f9ec0d24e3dcefc118f5dee138222cc7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/27340273363" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-06-11T10:28:13.000Z", "commit": "11b59d5682341b18ebec9da6fc21ee554d7927db", "fileid": "685ad69d061b12775c183bcf28a7982dc45461fc1830950a750c2aab9c9d3002", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/27340273363" } ] }