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

## Documentation for package ‘pmd’ version 0.1.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

getchain | Get reaction chain for specific mass to charge ratio
getcluster | Get Pseudo-Spectrum as peaks cluster based on pmd analysis.
getcorcluster | Get Pseudo-Spectrum as peaks cluster based on correlation analysis.
getpaired | Filter ions/peaks based on retention time hierarchical clustering, paired mass distances(PMD) and PMD frequency analysis.
getpmd | Get pmd for specific reaction
getrda | Perform structure/reaction directed analysis for mass only.
getreact | Get quantitative paired peaks list for specific reaction/pmd
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.
gettarget | Get multiple injections index for selected retention time
globalstd | GlobalStd algorithm with structure/reaction directed analysis
hmdb | A dataframe containing HMDB top 10000 unique accurate mass pmd and related reactions
hmdbp | A list dataset containing HMDB unique accurate mass pmd analysis results
keggrall | A dataframe containing reaction related accurate mass pmd and related reaction formula with KEGG ID
omics | A dataframe containing multiple reaction database ID and their related accurate mass pmd and related reactions
pcasf | Compare matrices using PCA similarity factor
plotpaired | Plot the mass pairs and high frequency mass distances
plotrtg | Plot the retention time group
plotsda | Plot the specific structure directed analysis(SDA) groups
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.