{ "_id": "6a21392bcd65a98ecbd276af", "Package": "metevalue", "Type": "Package", "Title": "E-Value in the Omics Data Association Studies", "Version": "0.2.4", "Date": "2023-05-26", "Authors@R": "c(person(\"Yifan\", \"Yang\", role = c(\"aut\", \"cre\",\"cph\"),\nemail = \"yfyang.86@hotmail.com\"),\nperson(\"Xiaoqing\", \"Pan\", role = \"aut\"),\nperson(\"Haoyuan\", \"Liu\", role = \"aut\"))", "Maintainer": "Yifan Yang ", "Description": "In the omics data association studies, it is common to\nconduct the p-value corrections to control the false\nsignificance. Beyond the P-value corrections, E-value is\nrecently studied to facilitate multiple testing correction\nbased on V. Vovk and R. Wang (2021) .\nThis package provides E-value calculation for DNA methylation\ndata and RNA-seq data. Currently, five data formats are\nsupported: DNA methylation levels using DMR detection tools\n(BiSeq, DMRfinder, MethylKit, Metilene and other DNA\nmethylation tools) and RNA-seq data. The relevant references\nare listed below: Katja Hebestreit and Hans-Ulrich Klein (2022)\n; Altuna Akalin et.al (2012)\n.", "License": "Apache License (>= 2)", "RoxygenNote": "7.2.1", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "LazyData": "true", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Author": "Yifan Yang [aut, cre, cph], Xiaoqing Pan [aut], Haoyuan Liu\n[aut]", "Packaged": { "Date": "2026-06-04 08:33:33 UTC", "User": "root" }, "Repository": "https://cran.r-universe.dev", "Date/Publication": "2023-05-26 14:20:06 UTC", "RemoteUrl": "https://github.com/cran/metevalue", "RemoteRef": "HEAD", "RemoteSha": "3d1acbdc404eae2df708abb79746528765fee636", "MD5sum": "0cb16b6ced24e81000301fe74714c3c1", "_user": "cran", "_type": "src", "_file": "metevalue_0.2.4.tar.gz", "_fileid": "68816d2196eb8c9b5f3cd4ed65a26321ece417c10e7c9951f02fbfe4e4e44fcd", "_filesize": 1846414, "_sha256": "68816d2196eb8c9b5f3cd4ed65a26321ece417c10e7c9951f02fbfe4e4e44fcd", "_created": 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"_registered": true, "_dependencies": [ { "package": "sqldf", "role": "Depends" }, { "package": "psych", "role": "Depends" }, { "package": "dplyr", "role": "Depends" }, { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "prettydoc", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 128, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/metevalue" }, "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", 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"table": true, "tojson": true }, { "name": "demo_biseq_methyrate", "title": "BiSeq Methyrate Demo Dataset", "object": "demo_biseq_methyrate", "class": [ "data.frame" ], "fields": [ "chr", "pos", "g1", "g1", "g1", "g1", "g1", "g2", "g2", "g2", "g2", "g2" ], "rows": 10502, "table": true, "tojson": true }, { "name": "demo_desq_out", "title": "DESeq Output Dataset", "object": "demo_desq_out", "class": [ "matrix", "array" ], "fields": [ "treated1fb", "treated2fb", "treated3fb", "untreated1fb", "untreated2fb", "untreated3fb", "untreated4fb" ], "rows": 8166, "table": true, "tojson": true }, { "name": "demo_DMRfinder_DMRs", "title": "DMRfinder Output Demo Dataset", "object": "demo_DMRfinder_DMRs", "class": [ "data.frame" ], "fields": [ "chr", "start", "end", "CpG", "Control.mu", "Exptl.mu", "Control..Exptl.diff", "Control..Exptl.pval" ], "rows": 757, "table": true, "tojson": true }, { "name": "demo_DMRfinder_rate_combine", "title": "DMRfinder Methyrate Demo Dataset", "object": 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"title": "Methyrate Dataset", "topics": [ "demo_methylkit_methyrate" ] }, { "page": "demo_metilene_input", "title": "Metilene Methyrate Demo Dataset", "topics": [ "demo_metilene_input" ] }, { "page": "demo_metilene_out", "title": "Metilene Demo Output Dataset", "topics": [ "demo_metilene_out" ] }, { "page": "evalue_buildin_sql", "title": "Build-in data process function", "topics": [ "evalue_buildin_sql" ] }, { "page": "evalue_buildin_var_fmt_nm", "title": "Build-in check file format function Perform the format check and data clean for the \"metilene\" or \"biseq\", \"DMRfinder\" or \"methylKit\" method correspondingly.", "topics": [ "evalue_buildin_var_fmt_nm" ] }, { "page": "metevalue.biseq", "title": "Calculate E-value of the BiSeq data format", "topics": [ "metevalue.biseq" ] }, { "page": "metevalue.biseq.chk", "title": "Check the BiSeq data format", "topics": [ "metevalue.biseq.chk" ] }, { "page": "metevalue.DMRfinder", "title": "Calculate E-value of the DMRfinder data format", "topics": [ "metevalue.DMRfinder" ] }, { "page": "metevalue.DMRfinder.chk", "title": "Check the DMRfinder data format", "topics": [ "metevalue.DMRfinder.chk" ] }, { "page": "metevalue.methylKit", "title": "Calculate E-value of the methylKit data format", "topics": [ "metevalue.methylKit" ] }, { "page": "metevalue.methylKit.chk", "title": "Check the methylKit data format", "topics": [ "metevalue.methylKit.chk" ] }, { "page": "metevalue.metilene", "title": "Calculate E-value of the Metilene data format", "topics": [ "metevalue.metilene" ] }, { "page": "metevalue.metilene.chk", "title": "Check the Metilene data format", "topics": [ "metevalue.metilene.chk" ] }, { "page": "metevalue.RNA_general", "title": "A general method to calculate the e-value for RNA-seq data.", "topics": [ "metevalue.RNA_general" ] }, { "page": "varevalue.metilene", "title": "Calculate E-value of the Metilene data", "topics": [ "varevalue.metilene" ] }, { "page": "varevalue.single_general", "title": "A general method to calculate the e-value for other DNA methylation tools not described above. The input data is the DNA methylation rates using the similar format with Metilene.", "topics": [ "varevalue.single_general" ] } ], "_rundeps": [ "bit", "bit64", "blob", "cachem", "chron", "cli", "cpp11", "DBI", "dplyr", "fastmap", "generics", "glue", "GPArotation", "gsubfn", "lattice", "lifecycle", "magrittr", "memoise", "mnormt", "nlme", "pillar", "pkgconfig", "proto", "psych", "R6", "rlang", "RSQLite", "sqldf", "tibble", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "metevalue.Rmd", "filename": "metevalue.html", "title": "E-value in DNA methylation studies", "engine": "knitr::rmarkdown", "headings": [ "Introductions", "Other Demos", "Call by files", "Call by R data frames", "Example: MethylKit", "Example: BiSeq", "Example: DMRfinder", "Example: Metilene", "Example: Other DNA methylation tools", "Example: RNA-seq data", "Misc", "Demo data", "Input Data Examples: MethylKit", "Input Data Examples: BiSeq", "Input Data Examples: DMRfinder", "Input Data Examples: Metilene", "Input Data Examples: Other DNA methylation tools", "Input Data Examples: RNA-seq data" ], "created": "2022-10-28 16:07:39", "modified": "2023-05-26 14:20:06", "commits": 4 } ], "_score": 2, "_indexed": true, "_nocasepkg": "metevalue", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.4", "date": "2026-06-04T08:35:51.000Z", "distro": "noble", "commit": "3d1acbdc404eae2df708abb79746528765fee636", "fileid": "8d1e847a74e0a18a7b712cef7ae957b9f312a2b210ce630b7fc9c69f62e8bb4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26940340050" }, { "r": "4.6.0", "os": "linux", "version": "0.2.4", "date": "2026-06-04T08:35:46.000Z", "distro": "noble", "commit": "3d1acbdc404eae2df708abb79746528765fee636", "fileid": "accacab3f312a11f49f49f0c8a83e537e2c0064b209095046b99a02a7f8011f9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26940340050" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.4", "date": "2026-06-04T08:35:54.000Z", "commit": "3d1acbdc404eae2df708abb79746528765fee636", "fileid": "e94f808fb7d3337ffe6b49de4d8c65e3ecd1bfb70d7ffbf08ff4005452395945", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26940340050" } ] }