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

## Documentation for package ‘dagLogo’ version 1.42.0

- 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'.