Man pages for symbioticMe/proBatch
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... |
