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. |