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.
process_qf              process_qf
processed_qf            processed_qf A QFeatures object prepared from
                        PEAKS data of Cathepsin data that has been
                        processed (imputation/normalization)
