| all_possible_8mers_from_228_library | all_possible_8mers_from_228_library All possible 8mers from the standard (as of 26April2024) 228 MSP-MS peptide library (This is equivalent to the result of mspms::calculate_all_cleavages(mspms::peptide_library$real_cleavage_seq,n=4)) vector of the 14 AA peptides used in the library. |
| calculate_all_cleavages | calculate_all_cleavages calculate all possible cleavages for a defined peptide library containing peptides of the same length. |
| check_file_is_valid_fragpipe | check_file_is_valid_fragpipe Check to make sure the input data looks like the expected FragPipe file. |
| check_file_is_valid_pd | check_file_is_valid_pd Check to make sure the input data looks like the expected ProteomeDiscoverer file. |
| colData | colData A tibble containing the colData associated with an experiment to proc |
| generate_report | generate_report |
| limma_stats | limma_stats |
| log2fc_t_test | log2fc_t_test |
| log2fc_t_test_data | log2fc_t_test_data A tibble containing the results of t-tests and log2fc compared to time 0 14,497 × 19 |
| mspms_tidy | mspms_tidy Convert a SummarizedExperiment object within a QFeatures object into a tidy tibble. |
| mspms_tidy_data | mspms_tidy_data A tibble containing tidy data derived from QFeatures object |
| peaks_prepared_data | peaks_prepared_data A QFeatures object prepared from PEAKS data of cathepsin data/. |
| peptide_library | peptide_library |
| plot_all_icelogos | plot_all_icelogos |
| plot_cleavages_per_pos | plot_cleavages_per_pos |
| plot_heatmap | plot_heatmap |
| plot_icelogo | plot_icelogo |
| plot_nd_peptides | plot_nd_peptides |
| plot_pca | plot_pca |
| plot_qc_check | plot_qc_check plot the the percentage of the peptide library undetected in each sample per each sample group. |
| plot_time_course | plot_time_course |
| plot_volcano | plot_volcano |
| prepare_fragpipe | prepare_fragpipe |
| prepare_pd | prepare_pd Prepare a label free quantification file exported from Proteome Discoverer for subsequent mspms analysis. |
| prepare_peaks | prepare_peaks Prepare a label free quantification file exported from PEAKS for subsequent mspms analysis. |
| processed_qf | processed_qf A QFeatures object prepared from PEAKS data of Cathepsin data that has been processed (imputation/normalization) |
| process_qf | process_qf |