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

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Documentation for package ‘pmd’ version 0.3.0

Help Pages

getcda Perform correlation directed analysis for peaks list.
getchain Get reaction chain for specific mass to charge ratio
getchainseq Get reaction pathway chains matching an ordered PMD pattern with quantifiers
getcorpseudospectrum Get Pseudo-Spectrum as peaks cluster based on correlation analysis.
gethomolog Find homologous series by a repeating PMD unit
getms2pmd read in MSP file as list for ms/ms annotation
getmspmd read in MSP file as list for EI-MS annotation
getnse Calculate Normalized Spectral Entropy (NSE)
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.
getsim Evaluate the similarity of two matrices or dataframes
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
MaConDa mass spectrometry contaminants database for PMD check
omics A dataframe containing multiple reaction database ID and their related accurate mass pmd and related reactions
parse_pmd_pattern Parse a PMD pattern string into a list of step specs
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
pmdchain Curated database of known multi-step reaction chains
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.