getpmd

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.

Miao YU

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

getpmd function

<dl><dt>list</dt>
<dd>a list with mzrt profile</dd>
<dt>pmd</dt>
<dd>a specific paired mass distance or a vector of pmds</dd>
<dt>rtcutoff</dt>
<dd>cutoff of the distances in retention time hierarchical clustering analysis, default 10</dd>
<dt>corcutoff</dt>
<dd>cutoff of the correlation coefficient, default NULL</dd>
<dt>digits</dt>
<dd>mass or mass to charge ratio accuracy for pmd, default 2</dd>
<dt>accuracy</dt>
<dd>measured mass or mass to charge ratio in digits, default 4</dd></dl>

Arguments

Get pmd for specific reaction — getpmd

<dl>

<dt>list</dt>
<dd>a list with mzrt profile</dd>


<dt>pmd</dt>
<dd>a specific paired mass distance or a vector of pmds</dd>


<dt>rtcutoff</dt>
<dd>cutoff of the distances in retention time hierarchical clustering analysis, default 10</dd>


<dt>corcutoff</dt>
<dd>cutoff of the correlation coefficient, default NULL</dd>


<dt>digits</dt>
<dd>mass or mass to charge ratio accuracy for pmd, default 2</dd>


<dt>accuracy</dt>
<dd>measured mass or mass to charge ratio in digits, default 4</dd>

</dl>

getpmd: Get pmd for specific reaction

Description

Usage

Value

Arguments

See Also

Examples