Proteome-class          Class 'Proteome'.
addScheme               Add a custom coloring or grouping scheme.
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'.
