GC/LC-MS Data Analysis for Environmental Science

batch | Get the MIR and related information from the files |

cbmd | Combine two data with similar retention time while different... |

findline | find line of the regression model for GC-MS |

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. |

getfeaturesanova | Get the features from anova, with p value, q value, rsd and... |

getfeaturest | Get the features from t test, with p value, q value, rsd and... |

getgrouprep | Get the report for samples with biological and technique... |

GetIntegration | GetIntegration was mainly used for get the intergration of... |

Getisotopologues | Get the selected isotopologues at certain MS data |

getmassdefect | Get mass defect with certain scaled factor |

getmassdiff | Isotope extraction for single group of samples with certain... |

getmd | Import data and return the annotated matrix for GC/LC-MS by... |

getQCraw | get the data of QC compound for a group of data |

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... |

getupload | Get the csv files to be submitted to Metaboanalyst |

Integration | Just intergrate data according to fixed rt and fixed noise... |

ma | filter data by average moving box |

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... |

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 xcmsset (or two) objects with... |

plotmrc | plot the diff scatter plot for one xcmsset objects with... |

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 xcmsset |

plotrsd | plot the rsd influnces of data |

plotrtms | Plot mass spectrum of certain retention time and return mass... |

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... |

plottic | Plot Total Ion Chromatogram (TIC) |

qbatch | Get the MIR from the file |

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... |

svadata | Filter the data with p value and q value |

svapca | Principal component analysis(PCA) for SVA corrected data and... |

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 |

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