Changelog • enviGCMS

CRAN

update MDplotR shiny documents
change class to inherits
fix save issue

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

goodpractice check
spell check

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

CRAN

change to formal group information for mzrt class
fix log infinite issue in plotridge
update list data

plotpeak for intensity of peaks across samples or samples across peaks
plotridge for ridgeline density plot
plotrug for 1-d density for multiple samples

add findlipid to annotate lipid class based on referenced Kendrick mass defect

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

remove dependency of genefilter
remove dependency of reshape2
remove dependency of ggplot2
remove dependency of ggridges

remove dependency of rcdk package
CRAN

fix ... issue

add functions to get and plot density weighted intensity
add pooled QC vignette
add plotcc to plot calibration curve

CRAN

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

CRAN

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

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

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

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

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

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

Major changes

update Vignette
add function for SCCP analysis
add peak list filter function based mass difference

Minor changes

add seealso

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

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