Function reference • pmd

All functions
`sda`	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
`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 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
`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.

Reference

All functions