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

addSchemeAdd a custom coloring or grouping scheme.
buildBackgroundModelBuild background models for DAU tests
buildZTestBackgroundModelBuild a background model for Z-test.
cleanPeptidesclean up peptides
colorsetsColor sets for visualization.
colorsets2retrieve color setting for logo visualization
dagBackground-classClass 'dagBackground'.
dagHeatmapVisualize daglogo using a heatmap.
dagLogoCreate sequence logo.
dagLogo-packageVisualize significant conserved peptide sequence pattern in...
dagPeptides-classClass 'dagPeptides'. An S4 class to represent formatted,...
ecoli.proteomeAn object of 'Proteome-class' representing the _Escherichia...
fetchSequenceFetch protein/peptide sequences and create a...
formatSequenceFormat already aligned peptide sequences.
getDataGet the data for visualization.
getGroupingSymbolGet character symbols for grouped amino acids
initiateBackgroundModelCreate a new 'dagBackground-class' object for 'testDAU'.
nameHashconvert group name to a single character
prepareProteomeprepare proteome for background building
prepareProteomeByFTPCreate an object of 'Proteome' Class.
prepareProteomeByUniProtWSPrepare a Proteome object for background building
Proteome-classClass 'Proteome'.
proteome.exampleAn object of 'Proteome-class' representing the subset of...
seq.exampleAn object of 'dagPeptides-class' representing acetylated...
testDAUDifferential usage test of amino acids or amino acid groups.
testDAUresults-classClass 'testDAUresults'.
jianhong/dagLogo documentation built on Nov. 6, 2019, 9:56 a.m.