GC/LC-MS Data Analysis for Environmental Science

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Documentation for package ‘enviGCMS’ version 0.7.1

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-- 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