GC/LC-MS Data Analysis for Environmental Science
Get the report for biological replicates.
Align multiple peaks list to one peak list
Convert an list object to csv file.
Get xcmsset object in one step with optimized methods.
Get XCMSnExp object in one step from structured folder path for xcms 3...
Generate the group level rsd and average intensity based on DoE,
Density weighted intensity for one sample
Get the features from anova, with p value, q value, rsd and power rest...
Get the features from t test, with p value, q value, rsd and power res...
Filter the data based on row and column index
Get chemical formula for mass to charge ratio.
Get the report for samples with biological and technique replicates in...
Impute the peaks list data
GetIntegration was mainly used for get the integration of certain ion'...
Get the selected isotopologues at certain MS data
Get the exact mass of the isotopologues from a chemical formula or rea...
Get mass defect with certain scaled factor
Import data and return the annotated matrix for GC/LC-MS by m/z range ...
Get the high order unit based Mass Defect
Get the raw Mass Defect
Get the mzrt profile and group information for batch correction and pl...
Annotation of MS1 data by compounds database by predefined paired mass...
read in MSP file as list for ms/ms or ms(EI) annotation
Get the mzrt profile and group information as a mzrt list and/or save ...
Get the mzrt profile and group information for batch correction and pl...
Covert the peaks list csv file into list
Get the overlap peaks by mass and retention time range
Merge positive and negative mode data
Get the index with power restriction for certain study with BH adjuste...
Compute pooled QC linear index according to run order
get the data of QC compound for a group of data
Get a mzrt list and/or save mz and rt range as csv file.
Perform peaks list alignment and return features table
Get the Relative Mass Defect
output the similarity of two dataset
Get the report for technique replicates.
Get the time series or two factor DoE report for samples with biologic...
Get the csv files from xcmsset/XCMSnExp/list object
Get the csv files to be submitted to Metaboanalyst
Get the csv files to be submitted to Metaboanalyst
plot scatter plot for rt-mz profile and output gif file for multiple g...
Just integrate data according to fixed rt and fixed noise area
filter data by average moving box
define the Mode function
Show MS/MS pmd annotation result
plot the calibration curve with error bar, r squared and equation.
plot the density for multiple samples
plot density weighted intensity for multiple samples
plot EIC and boxplot for all peaks and return diffreport
Plot the response group of GC-MS
plot the density of the GC-MS data with EM algorithm to separate the d...
Plot the heatmap of mzrt profiles
plot the information of integration
plot the slope information of integration
plot the kendrick mass defect diagram
plot the scatter plot for peaks list with threshold
plot the diff scatter plot for peaks list with threshold between two g...
plot GC/LC-MS data as a heatmap with TIC
Plot EIC of certain m/z and return dataframe for integration
plot GC/LC-MS data as scatter plot
plot the PCA for multiple samples
plot intensity of peaks across samples or samples across peaks
plot ridgeline density plot
Relative Log Abundance Ridge (RLAR) plots for samples or peaks
Relative Log Abundance (RLA) plots
plot the rsd influences of data in different groups
Plot mass spectrum of certain retention time and return mass spectrum ...
plot 1-d density for multiple samples
Plot the intensity distribution of GC-MS
Plot the background of data
plot GC-MS data as a heatmap for constant speed of temperature rising
Plot Total Ion Chromatogram (TIC)
Get the MIR from the file
Shiny application for interactive mass defect plots analysis
Shiny application for Short-Chain Chlorinated Paraffins analysis
Get the differences of two GC/LC-MS data
Plot the influences of DoE and Batch effects on each peaks
Surrogate variable analysis(SVA) to correct the unknown batch effects
Filter the data with p value and q value
Principal component analysis(PCA) for SVA corrected data and raw data
Filter the data with p value and q value and show them
Get the corrected data after SVA for metabolanalyst
Write MSP file for NIST search
Perform MS/MS X rank annotation for mgf file
Get the MIR and related information from the files
Combine two data with similar retention time while different mass rang...
Perform MS/MS dot product annotation for mgf file
Deprecated functions in package enviGCMS.
find line of the regression model for GC-MS
Find lipid class of metabolites base on referenced Kendrick mass defec...
Screen metabolites by Mass Defect
Screen organohalogen compounds by retention time, mass defect analysis...
Find PFCs based on mass defect analysis
Align two peaks vectors by mass to charge ratio and/or retention time
Align mass to charge ratio and/or retention time to remove redundancy
Get the peak list with blank samples' peaks removed
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.