Man pages for haibol2016/dagLogo
dagLogo: a bioconductor package for visualizeing conserved amino acid sequence pattern in groups based on probability theory
| addScheme | Add a custom coloring or grouping scheme. |
| availableSchemes | Get all predefined coloring and grouping schemes |
| buildBackgroundModel | Build background models for DAU tests |
| buildZTestBackgroundModel | Build a background model for Z-test. |
| cleanPeptides | clean up peptides |
| colorsets | Color sets for visualization. |
| colorsets2 | retrieve color setting for logo visualization |
| dagBackground-class | Class 'dagBackground'. |
| dagHeatmap | Visualize daglogo using a heatmap. |
| dagLogo | Create sequence logo. |
| dagLogo-package | Visualize significant conserved peptide sequence pattern in... |
| dagPeptides-class | Class 'dagPeptides'. An S4 class to represent formatted,... |
| ecoli.proteome | An object of 'Proteome-class' representing the _Escherichia... |
| fetchSequence | Fetch protein/peptide sequences and create a... |
| formatSequence | Format already aligned peptide sequences. |
| getData | Get the data for visualization. |
| getGroupingSymbol | Get character symbols for grouped amino acids |
| initiateBackgroundModel | Create a new 'dagBackground-class' object for 'testDAU'. |
| 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 | Class 'Proteome'. |
| proteome.example | An object of 'Proteome-class' representing the subset of... |
| seq.example | An object of 'dagPeptides-class' representing acetylated... |
| testDAU | Differential usage test of amino acids or amino acid groups. |
| testDAUresults-class | Class 'testDAUresults'. |
