# GC/LC-MS Data Analysis for Environmental Science

## Documentation for package ‘enviGCMS’ version 0.8.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

batch | Get the MIR and related information from the files
cbmd | Combine two data with similar retention time while different mass range
dotpanno | Perform MS/MS dot product annotation for mgf file
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
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
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
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
Integration | Just integrate data according to fixed rt and fixed noise area
list | Demo data
ma | filter data by average moving box
matrix | Demo raw data matrix
Mode | define the Mode function
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)
qbatch | Get the MIR from the file
runMDPlot | Shiny application for interactive mass defect plots analysis
runsccp | Shiny application for Short-Chain Chlorinated Paraffins analysis
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
TBBPA | Demo data for TBBPA metabolism in Pumpkin
writeMSP | Write MSP file for NIST search
xrankanno | Perform MS/MS X rank annotation for mgf file