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


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Documentation for package ‘pmd’ version 0.1.1

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getpaired Filter ions/peaks based on retention time hierarchical clustering, paired mass distances(PMD) and PMD frequency analysis.
getsda Perform structure/reaction directed analysis for peaks list.
getstd Find the independent ions for each retention time hierarchical clustering based on PMD relationship within each retention time cluster and isotope and return the index of the std data for each retention time cluster.
globalstd GlobalStd algorithm with structure/reaction directed analysis
plotpaired Plot the mass pairs and high frequency mass distances
plotrtg Plot the retention time group
plotstd Plot the std mass from GlobalStd algorithm
plotstdrt Plot the std mass from GlobalStd algorithm in certain retention time groups
plotstdsda Plot the std mass from GlobalStd algorithm in structure directed analysis(SDA) groups
runPMD Shiny application for PMD analysis
sda A dataset containing common Paired mass distances of substructure, ions replacements, and reaction
spmeinvivo A peaks list dataset containing 9 samples from 3 fish with triplicates samples for each fish from LC-MS.