Tools for the analysis of MSP-MS data

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Documentation for package ‘mspms’ version 1.1.0

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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