assess_missing          calculate the proportion of peptides with
                        missing values per group in a data set.
classify_bf_evidence    Classify Bayes factor into evidence categories
combine_tech_reps       Combine technical replicates
compare                 Compare peptide abundances between conditions
compare.data.frame      Default compare method for legacy data frames
compare_calls           compare sets of significant peptides called by
                        the used data
compare_many            compare many combinations of treatment and
                        control
estimate_result_clusters
                        plots a Figure of Merit curve to help estimate
                        the number of clusters in the results
fc_qqplot               plot qqplot of fold changes from a comparison
fold_change_matrix      returns a matrix of fold change values
get_bootstrap_percentile
                        get p values for contrast using boostrap t test
get_comparison          Get results for a specific comparison
get_kruskal_percentile
                        get p values for contrast using Kruskal-Wallis
                        test
get_peptide             Get results for a specific peptide
get_rp_percentile       get p values for contrast using Rank Products
                        test
get_sig_rows            works out if a peptide has at least one
                        significant value across the experiment
                        Composes a matrix of the 'metric' significance
                        values with peptides in rows, experiments in
                        columns and works out if each peptide row has a
                        value below the stated cut off
get_wilcoxon_percentile
                        get p values for contrast using Wilcoxon test
import_data             read data from a file
kmeans_by_selected_cols
                        Perform kmeans of a dataset using just data in
                        selected columns, then return matrices of all
                        columns
list2mat                converts a results object to a matrix as if for
                        direct use in external heatmap functions
long_results            Convert wide format results table to long
                        format
metrics                 reports metrics available for significance
                        values
missing_peptides_plot   plot the representation of peptides in each
                        group.
norm_qqplot             draw qqplots for data
p_value_hist            plot histograms of p-values for each test used
plot.pepdiff_data       Plot method for pepdiff_data
plot.pepdiff_results    Plot method for pepdiff_results
plot_bf_distribution    Bayes factor distribution plot
plot_distributions_simple
                        Simple distribution plot for pepdiff_data
plot_fc                 plot histogram of fold change distribution for
                        a comparison
plot_fc_distribution_new
                        Fold change distribution for pepdiff_results
plot_fit_diagnostics    Plot GLM fit diagnostics
plot_heatmap            makes heatmap from all experiments, filter on a
                        single metric and sig value
plot_kmeans             K-means cluster the data on the samples
plot_missingness_simple
                        Simple missingness plot for pepdiff_data
plot_pca                plots a pca on the treatment, seconds, bio-rep
plot_pca_simple         Simple PCA plot for pepdiff_data
plot_pvalue_histogram   P-value histogram for pepdiff_results
plot_quant_distributions
                        draw density plots for data
plot_result             plot the p-values against fold change for the
                        tests used in 'compare()'
plot_volcano_bf         Volcano plot for Bayes factor results
plot_volcano_new        Volcano plot for pepdiff_results
print.pepdiff_data      Print method for pepdiff_data
print.pepdiff_results   Print method for pepdiff_results
read_pepdiff            Read proteomics data into a pepdiff_data object
significant             Extract significant results
subset.pepdiff_data     Subset a pepdiff_data object
summary.pepdiff_data    Summary method for pepdiff_data
summary.pepdiff_results
                        Summary method for pepdiff_results
test_bayes_t            Bayes factor t-test for two groups
test_bootstrap_t        Bootstrap t-test for two groups
test_rankprod           Rank products test for two groups
test_wilcoxon           Wilcoxon rank-sum test for two groups
times_measured          calculate number of measurements of each
                        peptide in each treatment and time
times_measured_plot     plot the count of the number of times peptides
                        were measured.
volcano_plot            volcano plot the data
