Learn R Programming

enviGCMS: GC-MS Data Analysis for Environmental Science

enviGCMS provides functions for GC/LC-MS data analysis for environmental sciences.

Installation

You can either use the stable version of enviGCMS from CRAN,

install.packages("enviGCMS")

or the current development snapshot from this GitHub repository:

remotes::install_github("yufree/enviGCMS")

This package has removed the depends/suggests on xcms package as it is a package with too many unstable depends. If you need to use the functions in xcms, please find the release version of enviGCMS 0.7.4.

Usage

Check this vignette for Data analysis of GC-MS and LC-MS in Environmental Science.

Check this vignette for Pooled QC analysis in Environmental Science.

Detailed usage of functions in Environmental analysis could be found in this paper and the vignettes in this package.

Copy Link

Version

Install

install.packages('enviGCMS')

Monthly Downloads

519

Version

0.8.0

License

GPL-2

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/yufree/enviGCMS

Maintainer

Miao YU

Last Published

January 14th, 2025

Functions in enviGCMS (0.8.0)

read in MSP file as list for ms/ms or ms(EI) annotation

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.

Get the peak list with blank samples' peaks removed

Getisotopologues

Get the selected isotopologues at certain MS data

Align mass to charge ratio and/or retention time to remove redundancy

Get the features from t test, with p value, q value, rsd and power restriction

Get the MIR and related information from the files

Align two peaks vectors by mass to charge ratio and/or retention time

getfeaturesanova

Get the features from anova, with p value, q value, rsd and power restriction

Get the exact mass of the isotopologues from a chemical formula or reaction's isotope patterns with the highest abundances

Get mass defect with certain scaled factor

get the data of QC compound for a group of data

Align multiple peaks list to one peak list

Convert an list object to csv file.

Get the raw Mass Defect

Find PFCs based on mass defect analysis

Get the report for biological replicates.

Filter the data based on row and column index

Annotation of MS1 data by compounds database by predefined paired mass distance

Get the mzrt profile and group information as a mzrt list and/or save them as csv or rds for further analysis.

Get the mzrt profile and group information for batch correction and plot as a list directly from path with default setting

output the similarity of two dataset

plot the calibration curve with error bar, r squared and equation.

Get the Relative Mass Defect

Generate the group level rsd and average intensity based on DoE,

Get chemical formula for mass to charge ratio.

plot the density for multiple samples

Demo raw data matrix

Get the overlap peaks by mass and retention time range

Show MS/MS pmd annotation result

Find lipid class of metabolites base on referenced Kendrick mass defect

Get XCMSnExp object in one step from structured folder path for xcms 3.

Screen metabolites by Mass Defect

Get xcmsset object in one step with optimized methods.

Relative Log Abundance Ridge (RLAR) plots for samples or peaks

Get the report for samples with biological and technique replicates in different groups

Merge positive and negative mode data

Get the report for technique replicates.

plot density weighted intensity for multiple samples

plot EIC and boxplot for all peaks and return diffreport

Plot the background of data

Filter the data with p value and q value and show them

gettimegrouprep

Get the time series or two factor DoE report for samples with biological and technique replicates in different groups

plot GC-MS data as a heatmap for constant speed of temperature rising

Density weighted intensity for one sample

Impute the peaks list data

Get the corrected data after SVA for metabolanalyst

Get the csv files from xcmsset/XCMSnExp/list object

Get the mzrt profile and group information for batch correction and plot as a list for xcms 3 object

Covert the peaks list csv file into list

Get the csv files to be submitted to Metaboanalyst

Relative Log Abundance (RLA) plots

plot 1-d density for multiple samples

Plot the intensity distribution of GC-MS

Get the high order unit based Mass Defect

Import data and return the annotated matrix for GC/LC-MS by m/z range and retention time

Get the index with power restriction for certain study with BH adjusted p-value and certain power.

Get a mzrt list and/or save mz and rt range as csv file.

Perform peaks list alignment and return features table

plot intensity of peaks across samples or samples across peaks

plot ridgeline density plot

Filter the data with p value and q value

Plot Total Ion Chromatogram (TIC)

Get the csv files to be submitted to Metaboanalyst

Compute pooled QC linear index according to run order

Principal component analysis(PCA) for SVA corrected data and raw data

Get the MIR from the file

plot scatter plot for rt-mz profile and output gif file for multiple groups

plot the diff scatter plot for peaks list with threshold between two groups

plot the scatter plot for peaks list with threshold

plot the information of integration

Plot the heatmap of mzrt profiles

Shiny application for interactive mass defect plots analysis

Plot the response group of GC-MS

Shiny application for Short-Chain Chlorinated Paraffins analysis

Get the differences of two GC/LC-MS data

Short-Chain Chlorinated Paraffins(SCCPs) peaks information for quantitative analysis

plot the density of the GC-MS data with EM algorithm to separate the data into two log normal distribution.

plot GC/LC-MS data as a heatmap with TIC

Plot EIC of certain m/z and return dataframe for integration

filter data by average moving box

plot the slope information of integration

plot the kendrick mass defect diagram

Plot the influences of DoE and Batch effects on each peaks

Surrogate variable analysis(SVA) to correct the unknown batch effects

plot GC/LC-MS data as scatter plot

plot the PCA for multiple samples

plot the rsd influences of data in different groups

Plot mass spectrum of certain retention time and return mass spectrum vector (MSP file) for NIST search

Write MSP file for NIST search

Perform MS/MS X rank annotation for mgf file

Perform MS/MS dot product annotation for mgf file

define the Mode function

Just integrate data according to fixed rt and fixed noise area

enviGCMS-deprecated

Deprecated functions in package enviGCMS.

Combine two data with similar retention time while different mass range

find line of the regression model for GC-MS

GetIntegration was mainly used for get the integration of certain ion's chromatogram data and plot the data

Demo data for TBBPA metabolism in Pumpkin