GC/LC-MS Data Analysis for Environmental Science

---

Documentation for package ‘enviGCMS’ version 0.7.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

B C D F G I L M P Q R S T W X

-- B --

batch

Get the MIR and related information from the files

-- C --

cbmd	Combine two data with similar retention time while different mass range

-- D --

dotpanno

Perform MS/MS dot product annotation for mgf file

-- F --

findline	find line of the regression model for GC-MS
findlipid	Find lipid class of metabolites base on referenced Kendrick mass defect
findmet	Screen metabolites by Mass Defect
findohc	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.
findpfc	Find PFCs based on mass defect analysis

-- G --

getalign	Align two peaks vectors by mass to charge ratio and/or retention time
getalign2	Align mass to charge ratio and/or retention time to remove redundancy
getarea	Get the peak information from samples for SCCPs detection
getareastd	Get the peak information from SCCPs standards
getbgremove	Get the peak list with blank samples' peaks removed
getbiotechrep	Get the report for biological replicates.
getcompare	Align multiple peaks list to one peak list
getcsv	Convert an list object to csv file.
getdata	Get xcmsset object in one step with optimized methods.
getdata2	Get XCMSnExp object in one step from structured folder path for xcms 3.
getdoe	Generate the group level rsd and average intensity based on DoE,
getdwtus	Density weighted intensity for one sample
getfeaturesanova	Get the features from anova, with p value, q value, rsd and power restriction
getfeaturest	Get the features from t test, with p value, q value, rsd and power restriction
getfilter	Filter the data based on row and column index
getformula	Get chemical formula for mass to charge ratio.
getgrouprep	Get the report for samples with biological and technique replicates in different groups
getimputation	Impute the peaks list data
GetIntegration	GetIntegration was mainly used for get the integration of certain ion's chromatogram data and plot the data
Getisotopologues	Get the selected isotopologues at certain MS data
getmass	Get the exact mass of the isotopologues from a chemical formula or reaction's isotope patterns with the highest abundances
getmassdefect	Get mass defect with certain scaled factor
getmd	Import data and return the annotated matrix for GC/LC-MS by m/z range and retention time
getmdh	Get the high order unit based Mass Defect
getmdr	Get the raw Mass Defect
getmr	Get the mzrt profile and group information for batch correction and plot as a list directly from path with default setting
getms1anno	Annotation of MS1 data by compounds database by predefined paired mass distance
getMSP	read in MSP file as list for ms/ms or ms(EI) annotation
getmzrt	Get the mzrt profile and group information as a mzrt list and/or save them as csv or rds for further analysis.
getmzrt2	Get the mzrt profile and group information for batch correction and plot as a list for xcms 3 object
getmzrtcsv	Covert the peaks list csv file into list
getoverlappeak	Get the overlap peaks by mass and retention time range
getpn	Merge positive and negative mode data
getpower	Get the index with power restriction for certain study with BH adjusted p-value and certain power.
getpqsi	Compute pooled QC linear index according to run order
getQCraw	get the data of QC compound for a group of data
getrangecsv	Get a mzrt list and/or save mz and rt range as csv file.
getretcor	Perform peaks list alignment and return features table
getrmd	Get the Relative Mass Defect
getsccp	Quantitative analysis for short-chain chlorinated paraffins(SCCPs)
getsim	output the similarity of two dataset
gettechrep	Get the report for technique replicates.
gettimegrouprep	Get the time series or two factor DoE report for samples with biological and technique replicates in different groups
getupload	Get the csv files from xcmsset/XCMSnExp/list object
getupload2	Get the csv files to be submitted to Metaboanalyst
getupload3	Get the csv files to be submitted to Metaboanalyst
gifmr	plot scatter plot for rt-mz profile and output gif file for multiple groups

-- I --

Integration

Just integrate data according to fixed rt and fixed noise area

-- L --

list

Demo data

-- M --

ma	filter data by average moving box
Mode	define the Mode function

-- P --

plotanno	Show MS/MS pmd annotation result
plotcc	plot the calibration curve with error bar, r squared and equation.
plotden	plot the density for multiple samples
plotdwtus	plot density weighted intensity for multiple samples
plote	plot EIC and boxplot for all peaks and return diffreport
plotgroup	Plot the response group of GC-MS
plothist	plot the density of the GC-MS data with EM algorithm to separate the data into two log normal distribution.
plothm	Plot the heatmap of mzrt profiles
plotint	plot the information of integration
plotintslope	plot the slope information of integration
plotkms	plot the kendrick mass defect diagram
plotmr	plot the scatter plot for peaks list with threshold
plotmrc	plot the diff scatter plot for peaks list with threshold between two groups
plotms	plot GC/LC-MS data as a heatmap with TIC
plotmsrt	Plot EIC of certain m/z and return dataframe for integration
plotmz	plot GC/LC-MS data as scatter plot
plotpca	plot the PCA for multiple samples
plotpeak	plot intensity of peaks across samples or samples across peaks
plotridge	plot ridgeline density plot
plotridges	Relative Log Abundance Ridge (RLAR) plots for samples or peaks
plotrla	Relative Log Abundance (RLA) plots
plotrsd	plot the rsd influences of data in different groups
plotrtms	Plot mass spectrum of certain retention time and return mass spectrum vector (MSP file) for NIST search
plotrug	plot 1-d density for multiple samples
plotsms	Plot the intensity distribution of GC-MS
plotsub	Plot the background of data
plott	plot GC-MS data as a heatmap for constant speed of temperature rising
plottic	Plot Total Ion Chromatogram (TIC)

-- Q --

qbatch

Get the MIR from the file

-- R --

runMDPlot	Shiny application for interactive mass defect plots analysis
runsccp	Shiny application for Short-Chain Chlorinated Paraffins analysis

-- S --

sccp	Short-Chain Chlorinated Paraffins(SCCPs) peaks information for quantitative analysis
submd	Get the differences of two GC/LC-MS data
svabatch	Plot the influences of DoE and Batch effects on each peaks
svacor	Surrogate variable analysis(SVA) to correct the unknown batch effects
svadata	Filter the data with p value and q value
svapca	Principal component analysis(PCA) for SVA corrected data and raw data
svaplot	Filter the data with p value and q value and show them
svaupload	Get the corrected data after SVA for metabolanalyst

-- T --

TBBPA

Demo data for TBBPA metabolism in Pumpkin

-- W --

writeMSP

Write MSP file for NIST search

-- X --

xrankanno

Perform MS/MS X rank annotation for mgf file