trim.clone.trees

output of infer.clonal.models()$matched$merged.trees
or any list of trees produced by infer.clonal.models()$models

merged.trees:

remove clones that are found in
only one sample before comparing, default=T (used when reducing
merged trees. Set this to F to compare and reduce multiple samples
with the same tree to one sample

remove.sample.specific.clones:

Reduce clone trees produced by infer.clonal.models
to the core models, ie. ones that do not affect how clonal evolve
and branch across samples. This function will strip off the clones
that involve only one sample, any excluded nodes, and compare the trees
and keep only ones that are different. Return a list of merged.trees

clonevol performs clonal ordering and visualization using
the variant clustering results. It uses a bootstrap resampling
technique to estimate the cellular prevalence of the clones within
samples and probabilistically model clonal ordering constraints
(sum and cross rules), hence it tolerates error and variability
in cellular prevalence estimates of individual variants.

trim.clone.trees: Reduce clone trees to core trees after excluding clones that are present in only a single sample

Description

Usage

Arguments