Package index • protti

All functions
`analyse_functional_network()`	Analyse protein interaction network for significant hits
`anova_protti()`	Perform ANOVA
`assign_missingness()`	Assignment of missingness types
`assign_peptide_type()`	Assign peptide type
`barcode_plot()`	Barcode plot
`calculate_aa_scores()`	Calculate scores for each amino acid position in a protein sequence
`calculate_diff_abundance()`	Calculate differential abundance between conditions
`calculate_go_enrichment()`	Perform gene ontology enrichment analysis
`calculate_imputation()`	Sampling of values for imputation
`calculate_kegg_enrichment()`	Perform KEGG pathway enrichment analysis
`calculate_protein_abundance()`	Label-free protein quantification
`calculate_sequence_coverage()`	Protein sequence coverage
`calculate_treatment_enrichment()`	Check treatment enrichment
`correct_lip_for_abundance()`	Protein abundance correction for LiP-data
`create_queue()`	Creates a mass spectrometer queue for Xcalibur
`create_structure_contact_map()`	Creates a contact map of all atoms from a structure file
`create_synthetic_data()`	Creates a synthetic limited proteolysis proteomics dataset
`drc_4p()`	Dose response curve helper function
`drc_4p_plot()`	Plotting of four-parameter dose response curves
`extract_metal_binders()`	Extract metal-binding protein information from UniProt
`fetch_alphafold_aligned_error()`	Fetch AlphaFold aligned error
`fetch_alphafold_prediction()`	Fetch AlphaFold prediction
`fetch_chebi()`	Fetch ChEBI database information
`fetch_eco()`	Fetch evidence & conclusion ontology
`fetch_go()`	Fetch gene ontology information from geneontology.org
`fetch_kegg()`	Fetch KEGG pathway data from KEGG
`fetch_metal_pdb()`	Fetch structural information about protein-metal binding from MetalPDB
`fetch_mobidb()`	Fetch protein disorder and mobility information from MobiDB
`fetch_pdb()`	Fetch structure information from RCSB
`fetch_pdb_structure()`	Fetch PDB structure atom data from RCSB
`fetch_quickgo()`	Fetch information from the QuickGO API
`fetch_uniprot()`	Fetch protein data from UniProt
`fetch_uniprot_proteome()`	Fetch proteome data from UniProt
`filter_cv()`	Data filtering based on coefficients of variation (CV)
`find_all_subs()`	Find all sub IDs of an ID in a network
`find_chebis()`	Find ChEBI IDs for name patterns
`find_peptide()`	Find peptide location
`find_peptide_in_structure()`	Finds peptide positions in a PDB structure based on positional matching
`fit_drc_4p()`	Fitting four-parameter dose response curves
`impute()`	Imputation of missing values
`mako_colours`	Viridis colour scheme
`map_peptides_on_structure()`	Maps peptides onto a PDB structure or AlphaFold prediction
`metal_chebi_uniprot`	List of metal-related ChEBI IDs in UniProt
`metal_go_slim_subset`	Molecular function gene ontology metal subset
`metal_list`	List of metals
`normalise()`	Intensity normalisation
`parallel_create_structure_contact_map()`	Creates a contact map of all atoms from a structure file (using parallel processing)
`parallel_fit_drc_4p()`	Fitting four-parameter dose response curves (using parallel processing)
`peptide_profile_plot()`	Peptide abundance profile plot
`predict_alphafold_domain()`	Predict protein domains of AlphaFold predictions
`protti_colours`	Colour scheme for protti
`ptsi_pgk`	Structural analysis example data
`pval_distribution_plot()`	Plot histogram of p-value distribution
`qc_charge_states()`	Check charge state distribution
`qc_contaminants()`	Percentage of contaminants per sample
`qc_cvs()`	Check CV distribution
`qc_data_completeness()`	Data completeness
`qc_ids()`	Check number of precursor, peptide or protein IDs
`qc_intensity_distribution()`	Check intensity distribution per sample and overall
`qc_median_intensities()`	Median run intensities
`qc_missed_cleavages()`	Check missed cleavages
`qc_pca()`	Plot principal component analysis
`qc_peak_width()`	Peak width over retention time
`qc_peptide_type()`	Check peptide type percentage share
`qc_proteome_coverage()`	Proteome coverage per sample and total
`qc_ranked_intensities()`	Check ranked intensities
`qc_sample_correlation()`	Correlation based hirachical clustering of samples
`qc_sequence_coverage()`	Protein coverage distribution
`randomise_queue()`	Randomise samples in MS queue
`rapamycin_10uM`	Rapamycin 10 uM example data
`rapamycin_dose_response`	Rapamycin dose response example data
`read_protti()`	Read, clean and convert
`replace_identified_by_x()`	Replace identified positions in protein sequence by "x"
`scale_protti()`	Scaling a vector
`split_metal_name()`	Convert metal names to search pattern
`try_query()`	Query from URL
`ttest_protti()`	Perform Welch's t-test
`viridis_colours`	Viridis colour scheme
`volcano_plot()`	Volcano plot
`woods_plot()`	Woods' plot

Reference

All functions