NEWS
enviGCMS 0.9.0
Breaking changes
- Remove all deprecated functions from v0.7.x (32 functions including
getdata, getdata2, getmzrt2, svabatch, svaplot, etc.). Users should migrate to current API.
- Remove
Mode() (statistical mode function) -- unused internally since getmdg() moved to pmd package.
- Standardize API naming conventions:
- Intensity column renamed from
ins to intensity in getMSP() and writeMSP() spectra data.frames.
- Rename
Integration() to integration(), GetIntegration() to getintegration(), Getisotopologues() to getisotopologues() for consistent lowercase naming.
New features (merged from MSxplorer)
- Add
HRMF() for high-resolution mass filtering with forward/reverse scoring and Figure of Merit (FoM), based on Kwiecien et al. (2015). Uses Rdisop instead of rcdk/rJava -- no new hard dependencies.
- Add
getHRMF() for batch HRMF processing of entire MSP files.
- Add
plotEIC() for extracted ion chromatogram plotting from mzML/mzXML files using RaMS.
- Add
plotTopMS1Peaks() interactive Shiny app to extract top MS1 ions from MS2 chromatograms.
- Add
plotTopMS2Peaks() interactive Shiny app to extract top MS2 ions from MS1 chromatograms.
Bug fixes
- Fix
getmdh(): cbind.data.frame(mz, MD1, MD1) corrected to cbind.data.frame(mz, MD1, MD2) for ceiling method.
- Fix
runMDPlot(): filename case mismatch (MDPlot.rmd -> mdplot.Rmd).
- Fix
getdoe(): sum(NROW(lv) > 1) != 0 (always TRUE) corrected to NROW(lv) > 1.
- Fix
getMSP(): extract duplicated peak-parsing code into internal helper.
- Fix
getmzrtcsv(): remove broken cross-reference to deleted getmzrt.
Dependency changes
- Move
animation from Imports to Suggests (only used by gifmr()).
- Move
mixtools from Imports to Suggests (only used by getimputation()).
- Add
RaMS to Suggests for lightweight mzML/mzXML access (replaces MSnbase).
- Hard Imports reduced from 11 to 8 packages.
Code quality
- Add 67 unit tests across 8 test files (was 1 test).
- Refactor
HRMF() from 285-line monolith into 135-line function with 4 internal helpers.
- Remove 809 lines of dead deprecated code and 35 orphan man pages.
enviGCMS 0.8.0 (2025-01-14)
- remove the dependency of xcms package
- fix ppm issue in getpn
enviGCMS 0.7.4
- CRAN
- remove rdisop related example
- update citation
- remove dependency of xcms and msnbase
- add onAttach message for bioc packages
enviGCMS 0.7.3
- fix getalign2 to accept mz vector without ordering
- fix getalign ppm bug
enviGCMS 0.7.2
- adope MoNA msp format for getMSP
enviGCMS 0.7.1 (2023-02-06)
enviGCMS 0.7.0
- update MDplotR shiny documents
- change class to inherits
- fix save issue
enviGCMS 0.6.9
- update writeMSP function
- add findpfc to find potential PFCs
- add getpn to connect pos and neg mode data and return mzrt object
- add support for xcms 3 EIC extraction
- add getcompare to align multiple mzrt objects
enviGCMS 0.6.8
- goodpractice check
- spell check
enviGCMS 0.6.7
- fix bug in getpower function
- change default par parameters for plotmrc
- remove the export of deprecated function
- fix the typo in documents
- improve getMSP to fit MoNA MSP format
- add getalign function to align two peaks vectors and remove getoverlapmass, getoverlaprt
- modify getmass to accept negative value
- add getms1anno for MS1 annotation by local compounds database with predefined paired mass distances
- add support to save target data csv without change default name
- add retention time alignment function for peaks lists
- add getalign2 function to align mass to charge ratio, retention time for the same peak list, this function could be used to refine peaks list
- fix color issues in plotrla and plotridge function
enviGCMS 0.6.6 (2020-06-04)
enviGCMS 0.6.5
- change to formal group information for mzrt class
- fix log infinite issue in plotridge
- update list data
enviGCMS 0.6.4
- plotpeak for intensity of peaks across samples or samples across peaks
- plotridge for ridgeline density plot
- plotrug for 1-d density for multiple samples
enviGCMS 0.6.3
- add findlipid to annotate lipid class based on referenced Kendrick mass defect
enviGCMS 0.6.2
- add getMSP to read in EI-MS or MS/MS msp file as list for annotation
- add xrankanno and dotpanno function for MS/MS X Rank and dot product annotation
- add getrangecsv for MS2 mgf file extraction
enviGCMS 0.6.1
- remove dependency of genefilter
- remove dependency of reshape2
- remove dependency of ggplot2
- remove dependency of ggridges
enviGCMS 0.6.0 (2020-02-03)
- remove dependency of rcdk package
- CRAN
enviGCMS 0.5.9
enviGCMS 0.5.8
- add functions to get and plot density weighted intensity
- add pooled QC vignette
- add plotcc to plot calibration curve
enviGCMS 0.5.7 (2019-08-22)
enviGCMS 0.5.6
- fix group issue in mzrt object
- all the group info will be imported as character while user could change the character into dataframe
- export getmzrtcsv
- add findmet to export metabolites for certain compounds based on mass defect
- add demo data for TBBPA metabolites from this publication
enviGCMS 0.5.5 (2019-05-14)
enviGCMS 0.5.4
Major changes
- move dependances of xcms and MSnbase to suggest and remove the export for those functions
- introduce parallel computation in getdoe
- add demo data and organize examples
- add Relative Log Abundance (RLA) plots and Relative Log Abundance Ridge(RLA) plots
- add getcsv to save the list as csv file
- add getfilter to filter the list
- add getpower to deal with power analysis in metabolomics
- rewrite getmzrt and getdoe to make analysis easier
- deprecated getupload, getfeaturest and getfeaturesanova
- update vignettes
- add support for group dim larger than 2
enviGCMS 0.5.2
Major changes
- combine xcms and xcms 3 object function
- add support for single group plot
- add shiny application for mass defect analysis
- add function to compute high order mass defect
- add function to compare two peak list by overlap
- add function to output csv file from list object
- add function to perform pmd analysis
- add function to get chemical formula
- fix wrong object name in getmzrt/getmzrt2
- add options to export EIC object
- add function to screen organohalogen compounds
- add density plot for multiple samples
enviGCMS 0.5.0 (2018-04-25)
Major changes from last CRAN version 0.3.4
- use list to communicate results between function instead of xcms objects
- getdoe function to handle data for various experimental design
- add functions and shiny application for Short-Chain Chlorinated Paraffins analysis
- update the visualization function
- support xcms 3 new objects
enviGCMS 0.4.5
Major changes
- remove GlobalStd function and shiny application into pmd package
- remove batch correction and simulation function into mzrtsim package
- add shiny application for sccp analysis
- add deprecated function
- update vignettes
enviGCMS 0.4.4
Major changes
- Shiny application for GlobalStd
- New GlobalStd algorithm
- New paired analysis based on retention time hierarchical clustering, paired mass differences(PMD), PMD frequency analysis
- Remove mass defect related analysis
- Plot function for paired analysis
- Plot function for GlobalStd result
- Organize the codes
Minor changes
- Add Mode function
- reformat code by formatR package
enviGCMS 0.4.3
Major changes
- RT cluster analysis for tentative isotope, adducts, and neutral loss peaks detection
- Correlation analysis to select the feature peaks within rt groups
- Mass defect(cluster) analysis for homologous series detection
- Add csv file generation for simulation data
- Add heatmap for mzrt profile
- Add index to plotpca
Minor changes
- Fit xcms 3 new function in getdata2
- Change the default name for metaboanalyst
- remove nonascll in CITATION
- remove faahKO package and MSnbase version for cran check
enviGCMS 0.4.2
Major changes
- update Vignette
- add function for SCCP analysis
- add peak list filter function based mass difference
Minor changes
enviGCMS 0.4.1
Major changes
- add batch correction methods with p-value and q-value: sva, isva
- remove svadata and svaupload
- add mzrtsim to simulate mzrt profile
- add simmzrt to make simulation input data
- add rlaplot and ridgesplot to show the distribution of the data
Minor changes
enviGCMS 0.4.0
Major changes
- Add getdoe and remove former DoE related function
- Change the plot function from xcmsset based to list based
- Add support for xcms 3 function