Dependency Logo

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Documentation for package ‘DepLogo’ version 1.2.1

• 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