Man pages for TeamMacLean/pepdiff
Analysing TSL PRM Peptide Data
| assess_missing | calculate the proportion of peptides with missing values per... |
| combine_tech_reps | combine tech replicates into one biological replicate... |
| compare | compare the peptide quantities in two experiments |
| 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... |
| 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_kruskal_percentile | get p values for contrast using Kruskal-Wallis test |
| get_percentile_lowest_observed_value_iterative | get p values for contrast using normal percentile |
| 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... |
| get_wilcoxon_percentile | get p values for contrast using Wilcoxon test |
| import_data | read data from a file |
| is_useable | calculate the number of non- NA or NaNs in a vector |
| kmeans_by_selected_cols | Perform kmeans of a dataset using just data in selected... |
| list2mat | converts a results object to a matrix as if for direct use in... |
| long_results | convert wide format results table containing p-value... |
| matrix_data | convert dataframe to matrix |
| mean_fold_change | calculate mean fold change for peptide |
| metrics | reports metrics available for significance values |
| min_peptide_values | find minimal values for a peptide across replicates |
| missing_peptides_plot | plot the representation of peptides in each group. |
| norm_qqplot | draw qqplots for data |
| pipe | Pipe operator |
| plot_fc | plot histogram of fold change distribution for a comparison |
| plot_heatmap | makes heatmap from all experiments, filter on a single metric... |
| plot_kmeans | K-means cluster the data on the samples |
| plot_pca | plots a pca on the treatment, seconds, bio-rep |
| plot_quant_distributions | draw density plots for data |
| plot_result | plot the p-values against fold change for the tests used in... |
| p_value_hist | plot histograms of p-values for each test used |
| replace_vals | replace missing values in a vector with others provided |
| select_columns_for_contrast | extract data columns for specified contrast |
| times_measured | calculate number of measurements of each peptide in each... |
| times_measured_plot | plot the count of the number of times peptides were measured. |
| volcano_plot | volcano plot the data |
