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 |