{ "_id": "6a10ac1aacfb0bcc41cbfbf6", "Package": "pmd", "Type": "Package", "Title": "Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted\nAnalysis and Reactomics Analysis", "Version": "0.3.0", "Authors@R": "person(given = \"Miao\", family = \"YU\",\nrole = c(\"aut\", \"cre\"),\nemail = \"yufreecas@gmail.com\",\ncomment = c(ORCID = \"0000-0002-2804-6014\"))", "Description": "Paired mass distance (PMD) analysis proposed in Yu,\nOlkowicz and Pawliszyn (2018) \nand PMD based reactomics analysis proposed in Yu and Petrick\n(2020) for gas/liquid\nchromatography–mass spectrometry (GC/LC-MS) based non-targeted\nanalysis. PMD analysis including GlobalStd algorithm and\nstructure/reaction directed analysis. GlobalStd algorithm could\nfound independent peaks in m/z-retention time profiles based on\nretention time hierarchical cluster analysis and frequency\nanalysis of paired mass distances within retention time groups.\nStructure directed analysis could be used to find potential\nrelationship among those independent peaks in different\nretention time groups based on frequency of paired mass\ndistances. Reactomics analysis could also be performed to build\nPMD network, assign sources and make biomarker reaction\ndiscovery. GUIs for PMD analysis is also included as 'shiny'\napplications.", "URL": "https://yufree.github.io/pmd/", "BugReports": "https://github.com/yufree/pmd/issues", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "biocViews": "", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://yufree.r-universe.dev", "Date/Publication": "2026-04-22 13:55:27 UTC", "RemoteUrl": "https://github.com/yufree/pmd", "RemoteRef": "HEAD", "RemoteSha": "055816392e17674617d6ad563e380f7c91c9a9f1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 18:56:48 UTC", "User": "root" }, "Author": "Miao YU [aut, cre] (ORCID: )", "Maintainer": "Miao YU ", "MD5sum": "7b5fa29ccb7edc1eece0d33aecfdf384", "_user": "yufree", "_type": "src", "_file": "pmd_0.3.0.tar.gz", "_fileid": "7bbb7ef3331c8ac1c24042155bb3e98104251d2e8068a79fe8702fa1e20c74b4", "_filesize": 6094944, "_sha256": 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"artifact": "7168276425" }, { "job": 77444018920, "time": 115, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7168273695" }, { "job": 77444018978, "time": 163, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7168289005" } ], "_buildurl": "https://github.com/r-universe/yufree/actions/runs/26278684103", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/yufree/pmd", "_commit": { "id": "055816392e17674617d6ad563e380f7c91c9a9f1", "author": "ActionsGo Bot ", "committer": "ActionsGo Bot ", "message": "[Auto] update package website", "time": 1776866127 }, "_maintainer": { "name": "Miao YU", "email": "yufreecas@gmail.com", "orcid": "0000-0002-2804-6014" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "enviGCMS", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "yufree", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-17", "n": 5 } ], "_tags": [], "_topics": [ "mass-spectrometry", "metabolomics", "non-target" ], "_stars": 11, "_contributors": [ { "user": "yufree", "count": 236, "uuid": 2356936 } ], "_userbio": { "uuid": 2356936, "type": "user", "name": "Miao YU", "description": "Scientist @ JAX" }, "_downloads": { "count": 241, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/pmd" }, "_mentions": 3, "_devurl": "https://github.com/yufree/pmd", "_pkgdown": "https://yufree.github.io/pmd/", "_searchresults": 44, "_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/pmd.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/yufree/pmd", "_realowner": "yufree", "_cranurl": true, "_releases": [ { "version": "0.1.1", "date": "2018-12-02" }, { "version": "0.1.5", "date": "2019-08-22" }, { "version": "0.1.9", "date": "2020-06-04" }, { "version": "0.2.1", "date": "2021-01-22" }, { "version": "0.2.7", "date": "2025-01-17" } ], "_exports": [ "getcda", "getchain", "getchainseq", "getcorpseudospectrum", "gethomolog", "getms2pmd", "getmspmd", "getnse", "getpaired", "getpmd", "getpmddf", "getposneg", "getpseudospectrum", "getrda", "getreact", "getsda", "getsim", "getstd", "gettarget", "globalstd", "parse_pmd_pattern", "pcasf", "plotcn", "plotpaired", "plotrtg", "plotsda", "plotstd", "plotstdrt", "plotstdsda", "runPMD", "runPMDnet" ], "_datasets": [ { "name": "hmdb", "title": "A dataframe containing HMDB with unique accurate mass pmd with three digits frequency larger than 1 and accuracy percentage larger than 0.9.", "object": "hmdb", "class": [ "data.frame" ], "fields": [ "C", "H", "O", "N", "P", "S", "pmd", "pmd2", "percentage" ], "rows": 114824, "table": true, "tojson": true }, { "name": "keggrall", "title": "A dataframe containing reaction related accurate mass pmd and related reaction formula with KEGG ID", "object": "keggrall", "class": [ "data.frame" ], "fields": [ "rid", "rc", "ez", "ms1", "formula1", "ms2", "formula2", "pmd", "C", "H", "O", "N", "P", "S" ], "rows": 22336, "table": true, "tojson": true }, { "name": "MaConDa", "title": "mass spectrometry contaminants database for PMD check", "object": "MaConDa", "class": [ "data.frame" ], "fields": [ "id", "name", "formula", "exact_mass", "type_of_contaminant" ], "rows": 308, "table": true, "tojson": true }, { "name": "omics", "title": "A dataframe containing multiple reaction database ID and their related accurate mass pmd and related reactions", "object": "omics", "class": [ "data.frame" ], "fields": [ "X", "KEGG", "RHEA_ID", "DIRECTION", "MASTER_ID", "ec", "ecocyc", "macie", "metacyc", "reactome", "compounds", "pmd" ], "rows": 58050, "table": true, "tojson": true }, { "name": "sda", "title": "A dataset containing common Paired mass distances of substructure, ions replacements, and reaction", "object": "sda", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "PMD", "origin", "Ref.", "mode" ], "rows": 146, "table": true, "tojson": true }, { "name": "spmeinvivo", "title": "A peaks list dataset containing 9 samples from 3 fish with triplicates samples for each fish from LC-MS.", "object": "spmeinvivo", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "getcda", "title": "Perform correlation directed analysis for peaks list.", "topics": [ "getcda" ] }, { "page": "getchain", "title": "Get reaction chain for specific mass to charge ratio", "topics": [ "getchain" ] }, { "page": "getchainseq", "title": "Get reaction pathway chains matching an ordered PMD pattern with quantifiers", "topics": [ "getchainseq" ] }, { "page": "getcorpseudospectrum", "title": "Get Pseudo-Spectrum as peaks cluster based on correlation analysis.", "topics": [ "getcorpseudospectrum" ] }, { "page": "gethomolog", "title": "Find homologous series by a repeating PMD unit", "topics": [ "gethomolog" ] }, { "page": "getms2pmd", "title": "read in MSP file as list for ms/ms annotation", "topics": [ "getms2pmd" ] }, { "page": "getmspmd", "title": "read in MSP file as list for EI-MS annotation", "topics": [ "getmspmd" ] }, { "page": "getnse", "title": "Calculate Normalized Spectral Entropy (NSE)", "topics": [ "getnse" ] }, { "page": "getpaired", "title": "Filter ions/peaks based on retention time hierarchical clustering, paired mass distances(PMD) and PMD frequency analysis.", "topics": [ "getpaired" ] }, { "page": "getpmd", "title": "Get pmd for specific reaction", "topics": [ "getpmd" ] }, { "page": "getpmddf", "title": "Get pmd details for specific reaction after the removal of isotopouge.", "topics": [ "getpmddf" ] }, { "page": "getposneg", "title": "Link pos mode peak list with neg mode peak list by pmd.", "topics": [ "getposneg" ] }, { "page": "getpseudospectrum", "title": "Get Pseudo-Spectrum as peaks cluster based on correlation analysis.", "topics": [ "getpseudospectrum" ] }, { "page": "getrda", "title": "Perform structure/reaction directed analysis for mass only.", "topics": [ "getrda" ] }, { "page": "getreact", "title": "Get quantitative paired peaks list for specific reaction/pmd", "topics": [ "getreact" ] }, { "page": "getsda", "title": "Perform structure/reaction directed analysis for peaks list.", "topics": [ "getsda" ] }, { "page": "getsim", "title": "Evaluate the similarity of two matrices or dataframes", "topics": [ "getsim" ] }, { "page": "getstd", "title": "Identify standard ions through retention time clustering and PMD relationships", "topics": [ "getstd" ] }, { "page": "gettarget", "title": "Get multiple injections index for selected retention time", "topics": [ "gettarget" ] }, { "page": "globalstd", "title": "GlobalStd algorithm with structure/reaction directed analysis", "topics": [ "globalstd" ] }, { "page": "hmdb", "title": "A dataframe containing HMDB with unique accurate mass pmd with three digits frequency larger than 1 and accuracy percentage larger than 0.9.", "topics": [ "hmdb" ] }, { "page": "keggrall", "title": "A dataframe containing reaction related accurate mass pmd and related reaction formula with KEGG ID", "topics": [ "keggrall" ] }, { "page": "MaConDa", "title": "mass spectrometry contaminants database for PMD check", "topics": [ "MaConDa" ] }, { "page": "omics", "title": "A dataframe containing multiple reaction database ID and their related accurate mass pmd and related reactions", "topics": [ "omics" ] }, { "page": "parse_pmd_pattern", "title": "Parse a PMD pattern string into a list of step specs", "topics": [ "parse_pmd_pattern" ] }, { "page": "pcasf", "title": "Compare matrices using PCA similarity factor", "topics": [ "pcasf" ] }, { "page": "plotcn", "title": "plot PMD KEGG network for certain compounds and output network average distance and degree", "topics": [ "plotcn" ] }, { "page": "plotpaired", "title": "Plot the mass pairs and high frequency mass distances", "topics": [ "plotpaired" ] }, { "page": "plotrtg", "title": "Plot the retention time group", "topics": [ "plotrtg" ] }, { "page": "plotsda", "title": "Plot the specific structure directed analysis(SDA) groups", "topics": [ "plotsda" ] }, { "page": "plotstd", "title": "Plot the std mass from GlobalStd algorithm", "topics": [ "plotstd" ] }, { "page": "plotstdrt", "title": "Plot the std mass from GlobalStd algorithm in certain retention time groups", "topics": [ "plotstdrt" ] }, { "page": "plotstdsda", "title": "Plot the std mass from GlobalStd algorithm in structure directed analysis(SDA) groups", "topics": [ "plotstdsda" ] }, { "page": "runPMD", "title": "Shiny application for PMD analysis", "topics": [ "runPMD" ] }, { "page": "runPMDnet", "title": "Shiny application for PMD network analysis", "topics": [ "runPMDnet" ] }, { "page": "sda", "title": "A dataset containing common Paired mass distances of substructure, ions replacements, and reaction", "topics": [ "sda" ] }, { "page": "spmeinvivo", "title": "A peaks list dataset containing 9 samples from 3 fish with triplicates samples for each fish from LC-MS.", "topics": [ "spmeinvivo" ] } ], "_readme": "https://github.com/yufree/pmd/raw/HEAD/README.md", "_rundeps": [ "BH", "BiocParallel", "cli", "codetools", "cpp11", "data.table", "enviGCMS", "formatR", "futile.logger", "futile.options", "glue", "igraph", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "RColorBrewer", "Rcpp", "Rdisop", "rlang", "snow", "vctrs" ], "_vignettes": [ { "source": "globalstd.Rmd", "filename": "globalstd.html", "title": "Paired Mass Distance(PMD) analysis for GC/LC-MS based non-targeted analysis", "author": "Miao Yu", "engine": "knitr::rmarkdown", "headings": [ "Introduction of Paired Mass Distance analysis", "PMD from the same compound", "PMD from different compounds", "Data format", "GlobalStd algorithm", "STEP1: Retention time hierarchical clustering", "STEP2: Relationship among adducts, neutral loss, isotopologues and common fragments ions", "STEP3: Screen the independent peaks", "Extra filter with correlation coefficient cutoff", "Validation by principal components analysis(PCA)", "Comparison with other pseudo spectra extraction method", "Benchmark different datasets by Normalized Spectral Entropy (Sample Consistency Metric)", "Structure/Reaction directed analysis", "Structure/reaction directed analysis for peaks/compounds only data", "Wrap function for GlobalStd algorithm", "Use independent peaks for MS/MS validation (PMDDA)", "Shiny application", "Conclusion" ], "created": "2018-04-22 21:02:30", "modified": "2026-04-22 13:17:32", "commits": 27 }, { "source": "reactomics.Rmd", "filename": "reactomics.html", "title": "Reactomics", "author": "Miao Yu", "engine": "knitr::rmarkdown", "headings": [ "PMD network analysis", "Shiny application", "Tracing specific reaction paths and homologous series", "Source appointment", "Biomarker reaction", "Reactomics analysis for MS only data", "PMD Reaction Database" ], "created": "2020-08-12 03:57:33", "modified": "2026-04-22 02:09:57", "commits": 13 } ], "_score": 6.161966616364075, "_indexed": true, "_nocasepkg": "pmd", "_universes": [ "yufree" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.0", "date": "2026-05-22T19:03:45.000Z", "distro": "noble", "commit": "055816392e17674617d6ad563e380f7c91c9a9f1", "fileid": "bc2ac85c4990d7835650e6468482e5e0116742326a0c76b6f458447349ae0c28", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yufree/actions/runs/26278684103" }, { "r": "4.6.0", "os": "linux", "version": 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