dagLogo: a bioconductor package for visualizeing conserved amino acid sequence pattern in groups based on probability theory

Documentation for package ‘dagLogo’ version 1.26.0

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 'dagBackground'.
dagBackground-class	Class 'dagBackground'.
dagHeatmap	Visualize daglogo using a heatmap.
dagLogo	Create sequence logo.
dagPeptides	Class 'dagPeptides'. An S4 class to represent formatted, aligned peptides for dagLogo analysis.
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	Class 'Proteome'.
Proteome-class	Class 'Proteome'.
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 'testDAUresults'.
testDAUresults-class	Class 'testDAUresults'.