Package: enviGCMS 0.8.0

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_0.8.0.tar.gz
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enviGCMS_0.8.0.tgz(r-4.5-any)enviGCMS_0.8.0.tgz(r-4.4-any)
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enviGCMS.pdf |enviGCMS.html✨
enviGCMS/json (API)
NEWS

# 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 site:https://yufree.github.io

Datasets:

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

On CRAN:

environment mass-spectrometry metabolomics

6.66 score 17 stars 1 packages 30 scripts 388 downloads 1 mentions 61 exports 86 dependencies

Last updated 7 days agofrom:063acbd105. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 21 2025
R-4.5-win	OK	Mar 21 2025
R-4.5-mac	OK	Mar 21 2025
R-4.5-linux	OK	Mar 21 2025
R-4.4-win	OK	Mar 21 2025
R-4.4-mac	OK	Mar 21 2025
R-4.4-linux	OK	Mar 21 2025
R-4.3-win	OK	Mar 21 2025

Exports:findline findlipid findmet findohc findpfc getalign getalign2 getcompare getcsv getdoe getdwtus getfilter getformula getimputation GetIntegration Getisotopologues getmass getmassdefect getmdh getmdr getms1anno getMSP getmzrtcsv getoverlappeak getpn getpower getpqsi getrangecsv getretcor getrmd gifmr Integration ma Mode plotcc plotden plotdwtus plotgroup plothist plothm plotint plotintslope plotkms plotmr plotmrc plotms plotmz plotpca plotpeak plotridge plotridges plotrla plotrsd plotrug plotsms plotsub plott plottic runMDPlot runsccp writeMSP

Dependencies:animation askpass base64enc BH BiocParallel bslib cachem cli codetools colorspace cpp11 crosstalk curl data.table digest dplyr evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics ggplot2 glue gtable highr htmltools htmlwidgets httr igraph isoband jquerylib jsonlite kernlab knitr labeling lambda.r later lattice lazyeval lifecycle magick magrittr MASS Matrix memoise mgcv mime mixtools munsell nlme openssl pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp Rdisop rlang rmarkdown sass scales segmented snow stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

Data analysis of GC-MS and LC-MS in Environmental Science

Miao Yu

Rendered fromGCMSDA.Rmdusingknitr::rmarkdownon Mar 21 2025.

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

Pooled QC analysis

Miao Yu

Rendered fromPooledQC.Rmdusingknitr::rmarkdownon Mar 21 2025.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get the MIR and related information from the files	batch
Combine two data with similar retention time while different mass range	cbmd
Perform MS/MS dot product annotation for mgf file	dotpanno
find line of the regression model for GC-MS	findline
Find lipid class of metabolites base on referenced Kendrick mass defect	findlipid
Screen metabolites by Mass Defect	findmet
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 analysis	findpfc
Align two peaks vectors by mass to charge ratio and/or retention time	getalign
Align mass to charge ratio and/or retention time to remove redundancy	getalign2
Get the peak list with blank samples' peaks removed	getbgremove
Get the report for biological replicates.	getbiotechrep
Align multiple peaks list to one peak list	getcompare
Convert an list object to csv file.	getcsv
Get xcmsset object in one step with optimized methods.	getdata
Get XCMSnExp object in one step from structured folder path for xcms 3.	getdata2
Generate the group level rsd and average intensity based on DoE,	getdoe
Density weighted intensity for one sample	getdwtus
Get the features from anova, with p value, q value, rsd and power restriction	getfeaturesanova
Get the features from t test, with p value, q value, rsd and power restriction	getfeaturest
Filter the data based on row and column index	getfilter
Get chemical formula for mass to charge ratio.	getformula
Get the report for samples with biological and technique replicates in different groups	getgrouprep
Impute the peaks list data	getimputation
GetIntegration was mainly used for get the integration of certain ion's chromatogram data and plot the data	GetIntegration
Get the selected isotopologues at certain MS data	Getisotopologues
Get the exact mass of the isotopologues from a chemical formula or reaction's isotope patterns with the highest abundances	getmass
Get mass defect with certain scaled factor	getmassdefect
Import data and return the annotated matrix for GC/LC-MS by m/z range and retention time	getmd
Get the high order unit based Mass Defect	getmdh
Get the raw Mass Defect	getmdr
Get the mzrt profile and group information for batch correction and plot as a list directly from path with default setting	getmr
Annotation of MS1 data by compounds database by predefined paired mass distance	getms1anno
read in MSP file as list for ms/ms or ms(EI) annotation	getMSP
Get the mzrt profile and group information as a mzrt list and/or save them as csv or rds for further analysis.	getmzrt
Get the mzrt profile and group information for batch correction and plot as a list for xcms 3 object	getmzrt2
Covert the peaks list csv file into list	getmzrtcsv
Get the overlap peaks by mass and retention time range	getoverlappeak
Merge positive and negative mode data	getpn
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 order	getpqsi
get the data of QC compound for a group of data	getQCraw
Get a mzrt list and/or save mz and rt range as csv file.	getrangecsv
Perform peaks list alignment and return features table	getretcor
Get the Relative Mass Defect	getrmd
output the similarity of two dataset	getsim
Get the report for technique replicates.	gettechrep
Get the time series or two factor DoE report for samples with biological and technique replicates in different groups	gettimegrouprep
Get the csv files from xcmsset/XCMSnExp/list object	getupload
Get the csv files to be submitted to Metaboanalyst	getupload2
Get the csv files to be submitted to Metaboanalyst	getupload3
plot scatter plot for rt-mz profile and output gif file for multiple groups	gifmr
Just integrate data according to fixed rt and fixed noise area	Integration
Demo data	list
filter data by average moving box	ma
Demo raw data matrix	matrix
define the Mode function	Mode
Show MS/MS pmd annotation result	plotanno
plot the calibration curve with error bar, r squared and equation.	plotcc
plot the density for multiple samples	plotden
plot density weighted intensity for multiple samples	plotdwtus
plot EIC and boxplot for all peaks and return diffreport	plote
Plot the response group of GC-MS	plotgroup
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 profiles	plothm
plot the information of integration	plotint
plot the slope information of integration	plotintslope
plot the kendrick mass defect diagram	plotkms
plot the scatter plot for peaks list with threshold	plotmr
plot the diff scatter plot for peaks list with threshold between two groups	plotmrc
plot GC/LC-MS data as a heatmap with TIC	plotms
Plot EIC of certain m/z and return dataframe for integration	plotmsrt
plot GC/LC-MS data as scatter plot	plotmz
plot the PCA for multiple samples	plotpca
plot intensity of peaks across samples or samples across peaks	plotpeak
plot ridgeline density plot	plotridge
Relative Log Abundance Ridge (RLAR) plots for samples or peaks	plotridges
Relative Log Abundance (RLA) plots	plotrla
plot the rsd influences of data in different groups	plotrsd
Plot mass spectrum of certain retention time and return mass spectrum vector (MSP file) for NIST search	plotrtms
plot 1-d density for multiple samples	plotrug
Plot the intensity distribution of GC-MS	plotsms
Plot the background of data	plotsub
plot GC-MS data as a heatmap for constant speed of temperature rising	plott
Plot Total Ion Chromatogram (TIC)	plottic
Get the MIR from the file	qbatch
Shiny application for interactive mass defect plots analysis	runMDPlot
Shiny application for Short-Chain Chlorinated Paraffins analysis	runsccp
Short-Chain Chlorinated Paraffins(SCCPs) peaks information for quantitative analysis	sccp
Get the differences of two GC/LC-MS data	submd
Plot the influences of DoE and Batch effects on each peaks	svabatch
Surrogate variable analysis(SVA) to correct the unknown batch effects	svacor
Filter the data with p value and q value	svadata
Principal component analysis(PCA) for SVA corrected data and raw data	svapca
Filter the data with p value and q value and show them	svaplot
Get the corrected data after SVA for metabolanalyst	svaupload
Demo data for TBBPA metabolism in Pumpkin	TBBPA
Write MSP file for NIST search	writeMSP
Perform MS/MS X rank annotation for mgf file	xrankanno