Package: enviGCMS 0.9.0

Miao YU

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

Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.

Authors:Miao YU [aut, cre], Thanh Wang [ctb]

enviGCMS_0.9.0.tar.gz
enviGCMS_0.9.0.zip(r-4.7)enviGCMS_0.9.0.zip(r-4.6)enviGCMS_0.9.0.zip(r-4.5)
enviGCMS_0.9.0.tgz(r-4.6-any)enviGCMS_0.9.0.tgz(r-4.5-any)
enviGCMS_0.9.0.tar.gz(r-4.7-any)enviGCMS_0.9.0.tar.gz(r-4.6-any)
enviGCMS_0.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
enviGCMS/json (API)

# Install 'enviGCMS' in R:
install.packages('enviGCMS', repos = c('https://yufree.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yufree/envigcms/issues

Pkgdown/docs site:https://yufree.github.io

Datasets:
  • list - Demo data
  • matrix - Demo raw data matrix
  • sccp - Short-Chain Chlorinated Paraffins(SCCPs) peaks information for quantitative analysis
  • TBBPA - Demo data for TBBPA metabolism in Pumpkin

On CRAN:

Conda:

environmentmass-spectrometrymetabolomics

6.61 score 18 stars 2 packages 38 scripts 227 downloads 1 mentions 65 exports 23 dependencies

Last updated from:a24225dabb. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK169
source / vignettesOK230
linux-release-x86_64OK179
macos-release-arm64OK99
macos-oldrel-arm64OK120
windows-develOK119
windows-releaseOK119
windows-oldrelOK158
wasm-releaseOK154

Exports:findlinefindlipidfindmetfindohcfindpfcgetaligngetalign2getcomparegetcsvgetdoegetdwtusgetfiltergetformulagetHRMFgetimputationgetintegrationgetisotopologuesgetmassgetmassdefectgetmdhgetmdrgetms1annogetMSPgetmzrtcsvgetoverlappeakgetpngetpowergetpqsigetrangecsvgetretcorgetrmdgifmrHRMFintegrationmaplotccplotdenplotdwtusplotEICplotgroupplothistplothmplotintplotintslopeplotkmsplotmrplotmrcplotmsplotmzplotpcaplotpeakplotridgeplotridgesplotrlaplotrsdplotrugplotsmsplotsubplottplotticplotTopMS1PeaksplotTopMS2PeaksrunMDPlotrunsccpwriteMSP

Dependencies:BHBiocParallelclicodetoolscpp11data.tableformatRfutile.loggerfutile.optionsglueigraphlambda.rlatticelifecyclemagrittrMatrixpkgconfigRColorBrewerRcppRdisoprlangsnowvctrs

Data analysis of GC-MS and LC-MS in Environmental Science
Data analysis for single sample | Data structure of GC/LC-MS full scan mode | Data structure of GC-MS SIM mode | Data input | Visualization of mass spectrum data | Data analysis for influence from GC-MS | Data analysis for molecular isotope ratio | Quantitative analysis for short-chain chlorinated paraffins(SCCPs) | Data analysis for multiple samples | Wrap function for xcms package | Data imputation and filtering | Visualization of peaks list data | Summary
Rendered fromGCMSDA.Rmdusingknitr::rmarkdown

Last update: 2025-01-14
Started: 2016-01-12

Pooled QC analysis
Peaks profile | Density distribution | Relative Log Abundance (RLA) plots | Relative Log Abundance Ridge (RLAR) plots | Density Weighted Total Usable Signal | Run order effect analysis
Rendered fromPooledQC.Rmdusingknitr::rmarkdown

Last update: 2025-01-14
Started: 2019-11-08

Readme and manuals

Help Manual

Help pageTopics
find line of the regression model for GC-MSfindline
Find lipid class of metabolites base on referenced Kendrick mass defectfindlipid
Screen metabolites by Mass Defectfindmet
Screen organohalogen compounds by retention time, mass defect analysis and isotope relationship modified by literature report. Also support compounds with [M] and [M+2] ratio cutoff.findohc
Find PFCs based on mass defect analysisfindpfc
Align two peaks vectors by mass to charge ratio and/or retention timegetalign
Align mass to charge ratio and/or retention time to remove redundancygetalign2
Align multiple peaks list to one peak listgetcompare
Convert an list object to csv file.getcsv
Generate the group level rsd and average intensity based on DoE,getdoe
Density weighted intensity for one samplegetdwtus
Filter the data based on row and column indexgetfilter
Get chemical formula for mass to charge ratio.getformula
Batch High Resolution Mass Filtering for all compounds in an MSP filegetHRMF
Impute the peaks list datagetimputation
getintegration was mainly used for get the integration of certain ion's chromatogram data and plot the datagetintegration
Get the selected isotopologues at certain MS datagetisotopologues
Get the exact mass of the isotopologues from a chemical formula or reaction's isotope patterns with the highest abundancesgetmass
Get mass defect with certain scaled factorgetmassdefect
Get the high order unit based Mass Defectgetmdh
Get the raw Mass Defectgetmdr
Annotation of MS1 data by compounds database by predefined paired mass distancegetms1anno
read in MSP file as list for ms/ms or ms(EI) annotationgetMSP
Covert the peaks list csv file into listgetmzrtcsv
Get the overlap peaks by mass and retention time rangegetoverlappeak
Merge positive and negative mode datagetpn
Get the index with power restriction for certain study with BH adjusted p-value and certain power.getpower
Compute pooled QC linear index according to run ordergetpqsi
Get a mzrt list and/or save mz and rt range as csv file.getrangecsv
Perform peaks list alignment and return features tablegetretcor
Get the Relative Mass Defectgetrmd
plot scatter plot for rt-mz profile and output gif file for multiple groupsgifmr
High Resolution Mass Filtering (HRMF) for GC/LC HRMS dataHRMF
Just integrate data according to fixed rt and fixed noise areaintegration
Demo datalist
filter data by average moving boxma
Demo raw data matrixmatrix
plot the calibration curve with error bar, r squared and equation.plotcc
plot the density for multiple samplesplotden
plot density weighted intensity for multiple samplesplotdwtus
Plot extracted ion chromatograms from raw mzML/mzXML dataplotEIC
Plot the response group of GC-MSplotgroup
plot the density of the GC-MS data with EM algorithm to separate the data into two log normal distribution.plothist
Plot the heatmap of mzrt profilesplothm
plot the information of integrationplotint
plot the slope information of integrationplotintslope
plot the kendrick mass defect diagramplotkms
plot the scatter plot for peaks list with thresholdplotmr
plot the diff scatter plot for peaks list with threshold between two groupsplotmrc
plot GC/LC-MS data as a heatmap with TICplotms
plot GC/LC-MS data as scatter plotplotmz
plot the PCA for multiple samplesplotpca
plot intensity of peaks across samples or samples across peaksplotpeak
plot ridgeline density plotplotridge
Relative Log Abundance Ridge (RLAR) plots for samples or peaksplotridges
Relative Log Abundance (RLA) plotsplotrla
plot the rsd influences of data in different groupsplotrsd
plot 1-d density for multiple samplesplotrug
Plot the intensity distribution of GC-MSplotsms
Plot the background of dataplotsub
plot GC-MS data as a heatmap for constant speed of temperature risingplott
Plot Total Ion Chromatogram (TIC)plottic
Extract top MS1 ions from MS2 EIC interactivelyplotTopMS1Peaks
Extract top MS2 ions from MS1 EIC interactivelyplotTopMS2Peaks
Shiny application for interactive mass defect plots analysisrunMDPlot
Shiny application for Short-Chain Chlorinated Paraffins analysisrunsccp
Short-Chain Chlorinated Paraffins(SCCPs) peaks information for quantitative analysissccp
Demo data for TBBPA metabolism in PumpkinTBBPA
Write MSP file for NIST searchwriteMSP