Reference

All functions
MaConDa	mass spectrometry contaminants database for PMD check
getcda()	Perform correlation directed analysis for peaks list.
getchain()	Get reaction chain for specific mass to charge ratio
getcorpseudospectrum()	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
getpmddf()	Get pmd details for specific reaction after the removal of isotopouge.
getposneg()	Link pos mode peak list with neg mode peak list by pmd.
getpseudospectrum()	Get Pseudo-Spectrum as peaks cluster based on correlation analysis.
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()	Identify standard ions through retention time clustering and PMD relationships
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 frequency 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
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.