Man pages for DepLogo
Dependency Logo
| 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 |
| getPWM | Position weight matrix from DLData object |
| logo | Sequence logo |
| partition | Paritions data by most inter-dependent positions |
| plotBlocks | Plots blocks of data |
| plotDeparcs | Plots a graph representation of dependency values |
| plotDeplogo | Plot a dependency logo |
| plotDepmatrix | Plots a matrix representation of dependency values |
| replaceColors | Replaces colors in DLData object |
| revcom | Reverse complement |
| subBoxes | Plots weights as boxplots |
| subLines | Plots weights as lines |
| suggestColors | Suggests colors for symbols |
| summary.DLData | Summarizing DLData objects |
