Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis

Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) 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. A GUI for PMD analysis is also included as a 'shiny' application.


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pmd provides functions for Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) 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. A GUI for PMD analysis is also included as a shiny application.

Installation

You can install package from this GitHub repository:

devtools::install_github("yufree/pmd")

Usage

To perform GlobalStd algorithem, use the following code:

library(pmd)
data("spmeinvivo")
pmd <- getpaired(spmeinvivo, rtcutoff = 10, ng = 10)
std <- getstd(pmd)

To perform structure/reaction directed analysis, use the following code:

sda <- getsda(std)

To perform GlobalStd algorithem along with structure/reaction directed analysis, use the following code:

result <- globalstd(spmeinvivo)

To use the shiny application within the package, use the following code:

runPMD()

News

pmd 0.1.1

pmd 0.1.0

  • new package for paired mass distance analysis

Reference manual

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install.packages("pmd")

0.1.1 by Miao YU, 7 months ago


https://yufree.github.io/pmd


Report a bug at https://github.com/yufree/pmd/issues


Browse source code at https://github.com/cran/pmd


Authors: Miao YU [aut, cre]


Documentation:   PDF Manual  


GPL-2 license


Imports RColorBrewer, shiny, rmarkdown

Suggests knitr, enviGCMS


See at CRAN