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 |