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pmd
0.2.4
Reference
Articles
Paired Mass Distance(PMD) analysis for GC/LC-MS based non-targeted analysis
Reactomics
Changelog
Changelog
Source:
NEWS.md
pmd 0.2.4
add support for mass only data for quantitative reactomics analysis
add quantitative methods for dynamic pmds
add support for multiple pmds in getpmd function
update reactomics vignette to add more details for quantitative analysis of PMD
update getchain to handle large data
add mass defect filter for
getrda
and
getpaired
to retain reaction related PMDs
add parameter for
getrda
for pmd sets and mass defect table
change
getchain
corcutoff to 0.6
pmd 0.2.3
add MaConDa database
fix NULL default value issue in shiny apps
pmd 0.2.2
spell check
goodpractice package check
pmd 0.2.1
2021-01-21
CRAN
pmd 0.2.0
add option to skip sda in GlobalStd algorithm and set default to F
organize the R files
add vignette for reactomics analysis
add correlation directed analysis function
modified getcorcluster function to find independent peaks
add vignette section for reduced independent peaks selection in GlobalStd algorithm
fix the issue for getchain with multiple masses
fix the correlation issue in pos/neg linkage function
Output within RT clusters high frequencies PMD(s) as message for user to check
Change default ng to NULL in getpared function for automated generate parameter based on data
update with citation of cc paper
fix the bug in pmd ms/ms annotation due to the change of enviGCMS package
fix the order issue from CRAN
pmd 0.1.9
2020-06-04
CRAN
pmd 0.1.8
update kegg/hmdb database
update getsda to use largest average distance to find pmd frequency cutoff, more robust to large dataset
pmd 0.1.7
add function for pmd ms/ms annotation
add function to read in msp file as database
detach rcdk package
add function to link pos/neg by pmd
pmd 0.1.6
rewrite getchain to speed up
add shiny application pmdnet to perform PMD network analysis
add support for formula in getchain to find compounds ions
remove frequency cutoff in getsda and use PMD network clusters analysis to determine the cutoff
add merge feature for getcluster and such methods could be used to further reduce the GlobalStd peaks
remove hmdbp data since pmd network analysis could cover this topic
remove the dependence of group for quantitative paired peaks
improve shiny application for sda analysis
pmd 0.1.5
2019-08-22
CRAN
pmd 0.1.4
isotope selection improved to get rid of 1&2 issue
fix top issue in getsda
fix peak index issue in getcluster
add corcutoff for getpmd
pmd 0.1.3
speed up GlobalStd by mapply
add message for getrda
add hmdb pmd analysis results as dataset
add digits for mass accuracy
fix the ms1 larger issue in getpmd
add correlations in getpmd
add support for quantitative paired peaks list selection for specific reaction
add support for target pmd and compound analysis for reaction chain
pmd 0.1.2
update vignettes
change default ng value into auto-detection
add top option to limit sda output
add support for GlobalStd based targeted analysis
add support to extract specific pmd across different retention time groups
add PCA similarity factor function from EvolQG package
add support to export std peaks based on correlation within retention time group
add support to export index for peaks with highest intensity in peaks cluster
add support to use intensity data to refine GlobalStd results
add support to generate sda analysis for mass list only
#5
remove multi chargers with a strict rule
#4
add parameter selection part in vignette
#3
add support for peaks cluster output
#2
add support for formula generation in enviGCMS package
#1
pmd 0.1.1
2018-12-02
CRAN with ACA
publication
pmd 0.1.0
new package for paired mass distance analysis
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