NEWS.md

In yufree/enviGCMS: GC/LC-MS Data Analysis for Environmental Science

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

• CRAN

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

• CRAN

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

• remove dependency of rcdk package
• CRAN

enviGCMS 0.5.9

• fix ... issue

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

• CRAN

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

• CRAN

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

• CRAN

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

• add seealso

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

• revise citation keywords

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

yufree/enviGCMS documentation built on Sept. 12, 2023, 6:34 p.m.