General functions for the Center of Proteomics and Metabolomics (LUMC)

attr_rem | Remove attributes |

bubble_plot | Create bubble plots |

check_alignment | Check the alignment of mzXML files |

closest_match | Match list of standards to peak table |

diff_plot | Create difference plots |

equate | Quantile equatin |

flip_peaklist | Transpose a peaklist from XCMS |

get_mzxml_spectra | Retrieve MS1 spectra from a mzXML file |

merge_xcms_meta | Merge a XCMS output file with meta data |

m_pow_x | Modeling power |

msca | Multilevel Simultaneous Component Analysis (MSCA) |

msca_p | Multilevel Simultaneous Component Analysis (MSCA-P) |

msms_search_lipidmaps | Do a MSMS search on the Glycerophospholipid MS/MS Prediction... |

ms_search_lipidmaps | Do a MS search on the LMSD database from LipidMaps |

multiplot | Multiple plot function |

ncomp_opls | Find the optimal number of OPLS components |

o2pls | Orthogonal Projections to Latent Structures (OPLS) for a... |

o2pls_pred | Prediction function of the opls package |

opls | Orthogonal Projections to Latent Structures (OPLS) for a... |

opls_pred | Prediction function of the opls package |

pca_plots | Create nice PCA plots. |

perm_test | Permutation test for PLS and PLS-DA models |

plot_histogram | plot nice histogram |

pqn | Perform Probabilistic Quotient Normalization |

preprocess | Center and scale your data |

qc_plot | Create QC plots |

qc_rlsc | Perform QC-RLSC for batch correction of chromatographic... |

Rcpm-package | General functions for the Center of Proteomics and... |

reverse_predict | Do a reverse prediction on a linear regression |

simple_ellipse | Create a simple ellipse for a PCA score plot |

summary_fit | show summary of fit of a PCA model |

summary_fit_data | Reshape data frame for the summary_fit function. |

summary_se | Give a summary of a data frame |

tbl2roi | Convert a list of peaks (rt / m/z pairs) to a Region of... |

unmap | Dummy matrix for an outcome factor |

vip | Implementation of VIP (Variable Importance in Projection) for... |

vip_jh | Implementation of VIP (Variable Importance in Projection) for... |

xcmsraw_to_tbl | Convert raw data into a tibble of xcmsRaw objects. |

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