Proteome-class          Class 'Proteome'.
addScheme               Add a custom coloring or grouping scheme.
availableSchemes        Get all predefined coloring and grouping
                        schemes
buildBackgroundModel    Build background models for DAU tests
cleanPeptides           clean up peptides
colorsets2              retrieve color setting for logo visualization
dagBackground-class     Class 'dagBackground'.
dagHeatmap              Visualize daglogo using a heatmap.
dagLogo                 Create sequence logo.
dagPeptides-class       Class 'dagPeptides'. An S4 class to represent
                        formatted, aligned peptides for dagLogo
                        analysis.
ecoli.proteome          An object of 'Proteome-class' representing the
                        _Escherichia coli_ proteome.
fetchSequence           Fetch protein/peptide sequences and create a
                        'dagPeptides-class' object.
formatSequence          Format already aligned peptide sequences.
nameHash                convert group name to a single character
prepareProteome         prepare proteome for background building
prepareProteomeByFTP    Create an object of 'Proteome' Class.
prepareProteomeByUniProtWS
                        Prepare a Proteome object for background
                        building
proteome.example        An object of 'Proteome-class' representing the
                        subset of _Drosophila melanogaster_ proteome.
seq.example             An object of 'dagPeptides-class' representing
                        acetylated lysine-containing peptides.
testDAU                 Differential usage test of amino acids or amino
                        acid groups.
testDAUresults-class    Class 'testDAUresults'.
