pmd 0.2.7
- CRAN
- Change URL to doi for citation
- remove dependance of msnbase, function pmdanno has been moved to
rmwf package
pmd 0.2.6
- Add
getpmddf to show pmd details with given m/z only
data and m/z group information(optional, segmentation m/z group for
spatial reactomics analysis)
- Update reactomics vignette with section “Reactomics analysis for MS
only data” and showcase the quantitative analysis for certain PMD
- add support for mass only data for
getchain
pmd 0.2.5
- Add KEGG reaction class and enzyme number to the keggrall
database
- Fix url of demo data
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
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
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
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
pmd 0.1.0
- new package for paired mass distance analysis