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

## Documentation for package ‘pmd’ version 0.2.1

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

## Help Pages

getcda | Perform correlation directed analysis for peaks list.
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.
getms2pmd | read in MSP file as list for ms/ms annotation
getmspmd | read in MSP file as list for EI-MS annotation
getpaired | Filter ions/peaks based on retention time hierarchical clustering, paired mass distances(PMD) and PMD frequency analysis.
getpmd | Get pmd for specific reaction
getposneg | Link pos mode peak list with neg mode peak list by pmd.
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 with unique accurate mass pmd with three digits frequence larger than 1 and accuracy percentage larger than 0.9.
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
plotcn | plot PMD KEGG network for certain compounds and output network average distance and degree
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
pmdanno | Perform MS/MS pmd annotation for mgf file
runPMD | Shiny application for PMD analysis
runPMDnet | Shiny application for PMD network 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.