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

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-bind protein information from UniProt

fetch_alphafold_prediction()

Fetch AlphaFold prediction

fetch_chebi()

Fetch ChEBI database information

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 information from MobiDB

fetch_pdb()

Fetch structure information from RCSB

fetch_pdb_structure()

Fetch PDB structure atom data from RCSB

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 ChEBI sub IDs of an ID

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

map_peptides_on_structure()

Maps peptides onto a PDB structure or AlphaFold prediction

normalise()

Intensity normalisation

parallel_fit_drc_4p()

Fitting four-parameter dose response curves (using parallel processing)

peptide_profile_plot()

Peptide abundance profile plot

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_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

volcano_plot()

Volcano plot

woods_plot()

Woods' plot