adjust_batch_trend      adjust batch signal trend with the custom
                        (continuous) fit
center_peptide_batch_medians
                        Median centering of the peptides (per batch
                        median)
correct_batch_effects   Batch correction method allows correction of
                        continuous sigal drift within batch and
                        discrete difference across batches.
correct_with_ComBat     Adjusts for discrete batch effects using ComBat
create_peptide_annotation
                        Prepare peptide annotation from long format
                        data frame Create light-weight peptide
                        annotation data frame for selection of
                        illustrative proteins
date_to_sample_order    Convert date/time to POSIXct and rank samples
                        by it
dates_to_posix          Convert data/time to POSIXct
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
log_transform           Log transformation of the data, ensuring that
                        the row and column names are retained
long_to_matrix          Long to wide conversion
matrix_to_long          Wide to long conversion
normalize               Data normalization methods
normalize_data          Normalization brings the samples to the same
                        scale
normalize_sample_medians
                        Normalization by centering sample medians to
                        global median of the data
plot_PCA                plot PCA plot
plot_PVCA               Plot variance distribution by variable
plot_heatmap            Plot the heatmap of samples
plot_hierarchical_clustering
                        cluster the data matrix to visually inspect
                        which confounder dominates
plot_iRT                Plot iRT measurements
plot_peptide_corr_distribution
                        Plot distribution of peptide correlations
                        within one protein and between proteins
plot_peptides_of_one_protein
                        Plot peptides of one protein
plot_protein_corrplot   Peptide correlation matrix (heatmap)
plot_sample_corr_distribution
                        Create violin plot of correlation distribution
plot_sample_corr_heatmap
                        Sample correlation matrix (heatmap)
plot_sample_mean_or_boxplot
                        Plot per-sample mean or boxplot (showing median
                        and quantiles) vs order (if the real running
                        order available)
plot_single_feature     Plot peptide measurements
plot_spike_in           Plot spike-in measurements
plot_with_fitting_curve
                        Plot peptide measurements across multi-step
                        analysis
proBatch                proBatch: A package for diagnostics and
                        correction of batch effects, primarily in
                        proteomics
quantile_normalize      Quantile normalization of the data, ensuring
                        that the row and column names are retained
sample_annotation_to_colors
                        Generate colors for sample annotation
sample_color_scheme     Sample color annotation
