Man pages for hdng/clonevol
Clonal ordering and visualization
| adjust.clone.vaf | Adjust clone VAF according to significant different test... |
| assign.events.to.clones | Wrapper to assign events to clones in all merged trees This... |
| assign.events.to.clones.of.a.tree | Assign events to clones based on presence/absence of them... |
| boot.vaf.ci | Calculate CI for a cluster in a sample |
| clone.vaf.diff | Test if two clones have different VAFs Deprecated! |
| compare.clone.trees | Compare two clonal evolution trees |
| compare.clone.trees.removing.leaves | Compare two merged clonal evolution trees |
| convert.clone.to.branch | Create a tree from the merged.tree data.frame in clonevol... |
| convert.consensus.tree.clone.to.branch | Create trees for all merged.trees in clonevol output |
| createFishPlotObjects | Create a list of fishplot objects that can then be called |
| cross.rule.score | Apply cross rule to all clones in all matched models using... |
| cutBigValue | Replace values bigger than a cutoff by a value |
| determine.subclone | Determine which clones are subclone in a single sample, also... |
| draw.branch | Draw tree branch using polygon that allows for choosing... |
| draw.clone | Draw a bell/polygon representing a clone evolution, annotated... |
| 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,... |
| estimate.ccf | Calculate CI of CCF, pvals, etc. |
| estimate.clone.vaf | Estimate VAFs of clones/clusters from clonality analysis... |
| extract.mapped.events | Produce a data frame of events mapped to clone and associated... |
| find.matched.models | Find matched models between samples infer clonal evolution... |
| generate.boot | Generate and calculate bootstrap means for all clusters |
| generate.boot.nonparametric | Generate and calculate bootstrap means for all clusters... |
| generate.cloud.of.cells | Generate a cloud of circles to represent cell population |
| generate.fill.points | Generate fill points for bell/polygon plots |
| generateFishplotInputs | Generate fishplot ready data from clonevol clonal evolution... |
| germinate | Germinate a seed. |
| get.cell.frac.ci | Get cellular fraction confidence interval |
| get.clonevol.colors | Get the hex string of the preset colors optimized for... |
| get.model.max.p.value | Get the highest p.value of the test of Ho:ccf<0 This is the... |
| get.model.non.negative.ccf.prob | Get probability of a model for a sample as the product of... |
| get.subclones.across.samples | Get all set of subclones for all clone across samples... |
| import.tree | Import trees to clonevol |
| infer.clonal.models | Infer clonal structures and evolution models for multiple... |
| insert.lf | Insert line feed |
| 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 evolves to... |
| merge.all.matched.clone.trees | Recreate merged trees for matched models, given output of... |
| merge.clone.trees | Merge clonnal evolution trees from multiple samples into a... |
| merge.samples | Merge multi region samples into a meta sample |
| merge.variants.and.events | Merge variants and mapped events onto the same data frame... |
| plot.all.trees.clone.as.branch | Plot all branch-based consensus clonal evolution trees |
| plot.cell.population | Plot a tumor as a cloud of cells reflecting the cellular... |
| plot.clonal.models | Visualize clonal evolution models using various plots. |
| plot.clonevol.colors | Plot ClonEvol colors |
| plot.cloud.of.cells | Plot a cloud of cells |
| plot.cluster.flow | Plot the mean/median of the clusters of variants across... |
| plot.pairwise | Plot values of columns pairwise |
| plot.plant | Plot method for plant objects. |
| plot.tree | Plot clonal evolution tree |
| plot.tree.clone.as.branch | Plot a consensus tree using branch-based visualization |
| plot.variant.clusters | Plot variant clustering using combination of box, violin, and... |
| replaceNA | Replace NA with some value |
| rescale.vaf | Rescale VAF of subclones for visualzation purpose |
| save.clonevol.results | Save clonevol output to file |
| scale.cell.frac | Scale cellular fraction in a clonal architecture model |
| scale.sample.position | Prepare x positions to layout samples in bell plots |
| set.position | Set vertical position of clones within a sample clonal... |
| subclonal.test | Subclonal test of H0: |
| transfer.events.to.consensus.trees | Transfer driver variants/events from the cluster onto the... |
| trim.clone.trees | Reduce clone trees to core trees after excluding clones that... |
| write.tree | Write clonal evolution tree to file TODO: do! |
