# Dependency Logo

## Documentation for package ‘DepLogo’ version 1.2.2

- 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 | Plots a colorchart representation of a set of sequences
deprects | Rectangles of averaged colors
DLData | Create 'DLData' object
filter.by.conservation | Filters columns (sequence positions) by conservation
filter.by.dependencies | Filters columns (sequence positions) by dependency
filter.by.gaps | Filters columns (sequence positions) by gaps
filterColumns | Filters data columns by some filter function
getDeps | Compute dependencies between positions
getDeps.data.frame | Compute dependencies between positions
getDeps.DLData | Compute dependencies between positions
getPWM | Position weight matrix from DLData object
getPWM.DLData | Position weight matrix from DLData object
logo | Sequence logo
partition | Paritions data by most inter-dependent positions
partition.DLData | Paritions data by most inter-dependent positions
plotBlocks | Plots blocks of data
plotBlocks.DLData | Plots blocks of data
plotBlocks.list | Plots blocks of data
plotDeparcs | Plots a graph representation of dependency values
plotDeplogo | Plot a dependency logo
plotDeplogo.DLData | Plot a dependency logo
plotDepmatrix | Plots a matrix representation of dependency values
replaceColors | Replaces colors in DLData object
replaceColors.DLData | Replaces colors in DLData object
revcom | Reverse complement
revcom.DLData | Reverse complement
subBoxes | Plots weights as boxplots
subLines | Plots weights as lines
suggestColors | Suggests colors for symbols
suggestColors.DLData | Suggests colors for symbols
summary.DLData | Summarizing DLData objects