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

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Documentation for package ‘dagLogo’ version 1.47.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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 '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'.