{ "_id": "6a1aefff1d7bb097a09f6675", "Package": "swfdr", "Title": "Estimation of the science-wise false discovery rate and the\nfalse discovery rate conditional on covariates", "Version": "1.39.0", "Author": "Jeffrey T. Leek, Leah Jager, Simina M. Boca, Tomasz Konopka", "Maintainer": "Simina M. Boca , Jeffrey T. Leek\n", "Description": "This package allows users to estimate the science-wise\nfalse discovery rate from Jager and Leek, \"Empirical estimates\nsuggest most published medical research is true,\" 2013,\nBiostatistics, using an EM approach due to the presence of\nrounding and censoring. It also allows users to estimate the\nfalse discovery rate conditional on covariates, using a\nregression framework, as per Boca and Leek, \"A direct approach\nto estimating false discovery rates conditional on covariates,\"\n2018, PeerJ.", "License": "GPL (>= 3)", "URL": "https://github.com/leekgroup/swfdr", "BugReports": "https://github.com/leekgroup/swfdr/issues", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "biocViews": "MultipleComparison, StatisticalMethod, Software", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:45:07 UTC", "RemoteUrl": "https://github.com/bioc/swfdr", "RemoteRef": "HEAD", "RemoteSha": "658066d6abc1a261219b9c9d37ea33453de08150", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:43:17 UTC", "User": "root" }, "MD5sum": "d855a168757f094c4093dd9077af8d2d", "_user": "bioc", "_type": "src", "_file": "swfdr_1.39.0.tar.gz", "_fileid": "718aedb1beaca4b15529b68227f0e62ea31105e0821b80266830bc26d99b7e51", "_filesize": 968571, "_sha256": "718aedb1beaca4b15529b68227f0e62ea31105e0821b80266830bc26d99b7e51", "_created": "2026-05-30T09:43:17.000Z", "_published": "2026-05-30T14:11:11.254Z", "_jobs": [ { "job": 78640422108, "time": 127, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307416562" }, { "job": 78640422124, "time": 193, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307422671" }, { "job": 78640422134, "time": 172, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307421485" }, { "job": 78640422145, "time": 103, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308764916" }, { "job": 78640422143, "time": 119, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308766529" }, { "job": 78639776191, "time": 195, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307266115" }, { "job": 78640422121, "time": 89, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307413905" }, { "job": 78640422159, "time": 106, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307412669" }, { "job": 78640422173, "time": 92, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307411408" }, { "job": 78640422164, "time": 119, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307414405" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676647114", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/swfdr", "_commit": { "id": "658066d6abc1a261219b9c9d37ea33453de08150", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380307 }, "_maintainer": { "name": "Simina M. Boca", "email": "jtleek@gmail.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "stats4", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "dplyr", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "qvalue", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.39.0", "bioc": "3.24" }, { "branch": "release", "version": "1.38.0", "bioc": "3.23" } ], "_topics": [ "multiplecomparison", "statisticalmethod", "software" ], "_stars": 3, "_contributors": [ { "user": "tkonopka", "count": 19, "uuid": 7260190 }, { "user": "nturaga", "count": 4, "uuid": 2746443 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "jtleek", "count": 2, "uuid": 1571674 }, { "user": "vobencha", "count": 2, "uuid": 2466173 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 426, "source": "https://www.bioconductor.org/packages/stats/bioc/swfdr" }, "_mentions": 2, "_devurl": "https://github.com/leekgroup/swfdr", "_searchresults": 55, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/swfdr.html", "manual.pdf" ], "_homeurl": "https://github.com/leekgroup/swfdr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "calculateSwfdr", "lm_pi0", "lm_qvalue" ], "_datasets": [ { "name": "BMI_GIANT_GWAS_sample", "title": "Subset of SNPs from meta-analysis of BMI GWAS study.", "object": "BMI_GIANT_GWAS_sample", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "SNP", "A1", "A2", "Freq_MAF_Hapmap", "b", "se", "p", "N", "Freq_MAF_Int_Hapmap" ], "rows": 50000, "table": true, "tojson": true }, { "name": "journals_pVals", "title": "P-values from abstracts from articles in 5 biomedical journals (American Journal of Epidemiology, BMJ, JAMA, Lancet, New England Journal of Medicine), over 11 years (2000-2010).", "object": "journals_pVals", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "pvalue", "pvalueTruncated", "pubmedID", "year", "journal" ], "rows": 15653, "table": true, "tojson": true } ], "_help": [ { "page": "BMI_GIANT_GWAS_sample", "title": "Subset of SNPs from meta-analysis of BMI GWAS study.", "topics": [ "BMI_GIANT_GWAS_sample" ] }, { "page": "calculateSwfdr", "title": "Calculate the science-wise FDR (swfdr)", "topics": [ "calculateSwfdr" ] }, { "page": "get_number_decimals", "title": "Get number of decimals (i.e. return total number of digits after decimal point) for any vector of numbers in [0,1) if number of decimals <= 6", "topics": [ "get_number_decimals" ] }, { "page": "journals_pVals", "title": "P-values from abstracts from articles in 5 biomedical journals (American Journal of Epidemiology, BMJ, JAMA, Lancet, New England Journal of Medicine), over 11 years (2000-2010).", "topics": [ "journals_pVals" ] }, { "page": "lm_pi0", "title": "Estimation of pi0, proportion of p-values consistent with a null hypothesis", "topics": [ "lm_pi0" ] }, { "page": "lm_qvalue", "title": "Estimation of qvalues conditioned on covariates", "topics": [ "lm_qvalue" ] } ], "_readme": "https://github.com/bioc/swfdr/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "swfdrQ.Rmd", "filename": "swfdrQ.html", "title": "Computing q-values conditioned on covariates using swfdr", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "q-values without covariates", "Conceptual datasets", "pi0", "q-value", "Conditioning on covariates", "Conditioned pi0", "Conditioned q-values", "Conditioning on multiple covariates", "Conditioned pi0s with multiple covariates", "Conditioned q-values with multiple covariates", "Comparison with qvalue", "Discussion", "Technical notes", "Modeling resolution (argument lambda)", "Covariate matrix (argument X)", "Model type (argument type)", "Thresholding (argument threshold)", "Smoothing (argument smoothing)", "Smoothing degrees of freedom (argument smooth.df)", "References" ], "created": "2019-04-22 17:29:44", "modified": "2021-01-05 01:09:15", "commits": 2 }, { "source": "swfdrTutorial.Rmd", "filename": "swfdrTutorial.html", "title": "Tutorial for swfdr package", "author": "Jeff Leek, Simina Boca", "engine": "knitr::rmarkdown", "headings": [ "Package overview", "Estimating the science-wise false discovery rate", "Example: Estimate the swfdr based on p-values from biomedical journals", "The calculateSwfdr function", "Results from example dataset", "Estimating the proportion of true null hypothesis in the presence of covariates", "Example: Adjust for sample size and allele frequency in BMI GWAS meta-analysis", "The lm_pi0 function", "Results from BMI GWAS meta-analysis example", "References" ], "created": "2016-10-20 20:27:12", "modified": "2019-04-22 17:29:44", "commits": 16 } ], "_score": 6.421603926869831, "_indexed": true, "_nocasepkg": "swfdr", "_universes": [ "bioc", "leekgroup" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.39.0", "date": "2026-05-30T10:10:42.000Z", "distro": "noble", "commit": "658066d6abc1a261219b9c9d37ea33453de08150", "fileid": "16d64406788c319178f0604e6d2fff47f224cb5a48acd8ff4d21eed88934cb32", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676647114" }, { "r": "4.6.0", "os": "linux", "version": "1.39.0", "date": "2026-05-30T10:10:32.000Z", "distro": "noble", "commit": "658066d6abc1a261219b9c9d37ea33453de08150", "fileid": "5b1cf5c6543270341b38c6b21453f7064a95387b3f0c566fa71b8dff2ace7102", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676647114" }, { "r": "4.5.3", "os": "mac", "version": "1.39.0", "date": "2026-05-30T14:10:27.000Z", "commit": "658066d6abc1a261219b9c9d37ea33453de08150", "fileid": "9d284ce0295972a28836502aa7fb22d782222085d0a4cc34de6bac8578a09b28", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676647114" }, { "r": "4.6.0", "os": "mac", "version": "1.39.0", "date": "2026-05-30T14:10:44.000Z", "commit": "658066d6abc1a261219b9c9d37ea33453de08150", "fileid": "1ad99abcb6887185a7630f25d30ac4ac05de5b94b062d0a7244a52d64e0c378a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676647114" }, { "r": "4.6.0", "os": "wasm", "version": "1.39.0", "date": "2026-05-30T10:09:24.000Z", "commit": "658066d6abc1a261219b9c9d37ea33453de08150", "fileid": "aca56a431d80893d9a9353a9528a6769f6ee5f90e1fb1b3d9db7a7a29c8be2b1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676647114" }, { "r": "4.7.0", "os": "win", "version": "1.39.0", "date": "2026-05-30T10:08:47.000Z", "commit": "658066d6abc1a261219b9c9d37ea33453de08150", "fileid": "9c05ace9c663724e8f9774c5e24957cb8cf1b063c0a4b8b91cf207542016f37c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676647114" }, { "r": "4.5.3", "os": "win", "version": "1.39.0", "date": "2026-05-30T10:08:36.000Z", "commit": "658066d6abc1a261219b9c9d37ea33453de08150", "fileid": "615d42e8e3d75f239b79c9fa3d1cec2cd18a36c87bf3780a8248efd3aedaad38", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676647114" }, { "r": "4.6.0", "os": "win", "version": "1.39.0", "date": "2026-05-30T10:09:11.000Z", "commit": "658066d6abc1a261219b9c9d37ea33453de08150", "fileid": "3491fb3210f98ac9614740190795cb16e04e3c676351666833996e8570854305", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676647114" } ] }