Man pages for hadaxu/clonevol-mirror
What the package does (one line)
| adjust.clone.vaf | Adjust clone VAF according to significant different test... |
| boot.vaf.ci | Calculate CI for a cluster in a sample |
| clone.vaf.diff | Test if two clones have different VAFs |
| cutBigValue | Replace values bigger than a cutoff by a value |
| draw.clone | Draw a polygon representing a clone evolution, annotated with... |
| draw.sample.clones | Draw clonal structures/evolution of a single sample |
| draw.sample.clones.all | Draw all enumerated clonal models for a single sample |
| enumerate.clones | Enumerate all possible clonal structures for a single sample,... |
| enumerate.clones.absolute | Enumerate all possible clonal structures for a single sample,... |
| enumerate.clones.monoclonal | (Deprecated) Enumerate all possible clonal structures for a... |
| estimate.clone.vaf | Estimate VAFs of clones/clusters from clonality analysis... |
| find.matched.models | Find matched models between samples infer clonal evolution... |
| find.matched.models.1 | (Deprecated) Find matched models between samples infer clonal... |
| generate.boot | Generate and calculate bootstrap means for each cluster |
| infer.clonal.models | Infer clonal structures and evolution models for multiple... |
| infer.clonal.models.2 | (Deprecated) This function does not work well for >=3 samples... |
| infer.clonal.models.absolute | Infer clonal structures and evolution models for multiple... |
| is.ancestor | Check if clone a is ancestor of clone b in the clonal... |
| make.clonal.data.frame | Create a data frame to hold clonal structure of a single... |
| make.graph | Construct igraph object from clonal structures of a sample |
| match.sample.clones | Check if two clonal structures are compatible (one evolve to... |
| plot.clonal.models | Plot evolution models (polygon plots and trees) for multi... |
| plot.tree | Plot clonal evolution tree |
| replaceNA | Replace NA with some value |
| rescale.vaf | Rescale VAF of subclones s.t. total VAF must not exceed... |
| scale.cell.frac | Scale cellular fraction in a clonal architecture model |
| set.position | Set vertical position of clones within a sample clonal... |
| subclonal.test | Subclonal test H0: mean_X1 + mean_X2 <= mean_X |
| write.tree | Write clonal evolution tree to file TODO: do! |
