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| batch | Get the MIR and related information from the files |
| cbmd | Combine two data with similar retention time while different mass range |
| findline | find line of the regression model for GC-MS |
| getarea | Get the peak information from sampels 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. |
| 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 | Filter the data based on DoE, rsd, intensity |
| 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 |
| 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 intergration of certain ion's chromatogram data and plot the data |
| Getisotopologues | Get the selected isotopologues at certain MS data |
| 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 |
| getmr | Get the mzrt profile and group information for batch correction and plot as a list directly from path with default setting |
| getmzrt | Get the mzrt profile and group information for batch correction and plot as a list |
| 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 |
| getQCraw | get the data of QC compound for a group of data |
| 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 to be submitted to Metaboanalyst |
| getupload2 | Get the csv files to be submitted to Metaboanalyst |
| gifmr | plot scatter plot for rt-mz profile and output gif file for mutiple groups |
| Integration | Just intergrate data according to fixed rt and fixed noise area |
| ma | filter data by average moving box |
| Mode | define the Mode function |
| 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 seperate the data into two log normal distribution. |
| plothm | Plot the heatmap of mzrt profiles |
| plotint | plot the information of intergretion |
| plotintslope | plot the slope information of intergretion |
| plotkms | plot the kendrick mass defect diagram |
| plotmr | plot the scatter plot for peaks list with threshold |
| plotmrc | plot the diff scatter plot for one xcmsset objects 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 intergration |
| plotmz | plot GC/LC-MS data as scatter plot |
| plotpca | plot the PCA of list |
| plotrsd | plot the rsd influnces of data in different groups |
| plotrtms | Plot mass spectrum of certain retention time and return mass spectrum vector (MSP file) for NIST search |
| plotsms | Plot the intensity distribution of GC-MS |
| plotsub | Plot the backgrond 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 |
| runsccp | Shiny application for Short-Chain Chlorinated Paraffins analysis |
| sccp | Short-Chain Chlorinated Paraffins(SCCPs) peaks infomation for quantitative analysis |
| submd | Get the differences of two GC/LC-MS data |
| svabatch | Plot the influnces 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 |
| writeMSP | Write MSP files for NIST search |