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Documentation for package ‘DepLogo’ version 1.0

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Alphabet built alphabet
alphabet.dna DNA alphabet
alphabet.dna.gap DNA alphabet with gaps
alphabet.protein Amino acid alphabet
alphabet.protein.gap Amino acid alphabet with gaps
alphabet.rna RNA alphabet
alphabet.rna.gap RNA alphabet with gaps
colorchart Plot a colorchart representation of a set of sequences.
deprects Rectangles of averaged colors
DLData Create 'DLData' object
filter.by.conservation Filter columns (sequence positions) by conservation
filter.by.dependencies Filter columns (sequence positions) by dependency
filter.by.gaps Filter columns (sequence positions) by gaps
filterColumns Filter data columns by some filter function
getDeps Compute dependencies between positions
getPWM Position weight matrix from DLData object
logo Sequence logo
partition Parition data by most inter-dependent positions
plotBlocks Plots blocks of data
plotDeparcs Plot a graph representation of dependency values.
plotDeplogo Plot a dependency logo
plotDepmatrix Plot a matrix representation of dependency values.
replaceColors Replace colors in DLData object
revcom Reverse complement
subBoxes Plot weights as boxplots
subLines Plot weights as lines
suggestColors Suggest colors for symbols
summary.DLData Summarizing DLData objects