# Dependency Logo

## Documentation for package ‘DepLogo’ version 1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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