Tools for Diagnostics and Corrections of Batch Effects in Proteomics

calculate_feature_CV | Calculate CV distribution for each feature |

calculate_peptide_corr_distr | Calculate peptide correlation between and within peptides of... |

calculate_PVCA | Calculate variance distribution by variable |

calculate_sample_corr_distr | Calculates correlation for all pairs of the samples in data... |

check_sample_consistency | Check if sample annotation is consistent with data matrix and... |

color_list_to_df | Color list to data frame |

correct_batch_effects | Batch correction of normalized data |

create_peptide_annotation | Prepare peptide annotation from long format data frame Create... |

dates_to_posix | Convert data/time to POSIXct |

date_to_sample_order | Convert date/time to POSIXct and rank samples by it |

define_sample_order | Defining sample order internally |

example_peptide_annotation | Peptide annotation data |

example_proteome | Example protein data in long format |

example_proteome_matrix | Example protein data in matrix |

example_sample_annotation | Sample annotation data version 1 |

feature_level_diagnostics | Ploting peptide measurements |

fit_nonlinear | Fit a non-linear trend (currently optimized for LOESS) |

generate_colors_for_numeric | Generates color vector from continous palette |

long_to_matrix | Long to wide data format conversion |

matrix_to_long | Wide to long conversion |

merge_rare_levels | Replaces rare levels with other |

normalize | Data normalization methods |

plot_corr_matrix | Visualise correlation matrix |

plot_CV_distr | Plot CV distribution to compare various steps of the analysis |

plot_CV_distr.df | Plot the distribution (boxplots) of per-batch per-step CV of... |

plot_heatmap_diagnostic | Plot the heatmap of samples (cols) vs features (rows) |

plot_heatmap_generic | Plot the heatmap |

plot_hierarchical_clustering | cluster the data matrix to visually inspect which confounder... |

plot_PCA | plot PCA plot |

plot_peptide_corr_distribution | Create violin plot of peptide correlation distribution |

plot_protein_corrplot | Peptide correlation matrix (heatmap) |

plot_PVCA | Plot variance distribution by variable |

plot_PVCA.df | plot PVCA, when the analysis is completed |

plot_sample_corr_distribution | Create violin plot of sample correlation distribution |

plot_sample_corr_heatmap | Sample correlation matrix (heatmap) |

plot_sample_mean_or_boxplot | Plot per-sample mean or boxplots for initial assessment |

plot_split_violin_with_boxplot | Plot split violin plot (convenient to compare distribution... |

prepare_PVCA_df | prepare the weights of Principal Variance Components |

proBatch | proBatch: A package for diagnostics and correction of batch... |

sample_annotation_to_colors | Generate colors for sample annotation |

transform_raw_data | Functions to log transform raw data before normalization and... |

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