Package: pmd
Type: Package
Title: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted
        Analysis and Reactomics Analysis
Version: 0.2.7
Authors@R: person(given = "Miao", family = "YU",
        role = c("aut", "cre"), 
        email = "yufreecas@gmail.com",
        comment = c(ORCID = "0000-0002-2804-6014"))
Description: Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.
URL: https://yufree.github.io/pmd/
BugReports: https://github.com/yufree/pmd/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: knitr, shiny, rmarkdown
VignetteBuilder: knitr
biocViews:
Depends: R (>= 3.5.0)
Imports: RColorBrewer, stats, graphics, utils, igraph, enviGCMS
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-01-15 18:31:33 UTC; yufree
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>)
Maintainer: Miao YU <yufreecas@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-15 19:40:05 UTC
Built: R 4.6.0; ; 2026-04-23 03:44:13 UTC; windows
