determine.subclone

data frame of subclonal structure as output of enumerate.clones
v must have row.names = v$lab

label of the clone where it and its decendent clones will be
evaluated. This is often the root of the tree

Determine which clones are subclone or founder clone or both
or none subclones are identified based on cellular
fractions of the ancestor clones. Eg. if a clone is a subclone, all of its
decendent clones are subclone. If a clone is not a subclone and has zero
cell frac, its only decendent clone is not a subclone
founder clones are identified as clones whose cell frac is non-zero and whose
parent has zero cell frac

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.

Ha X. Dang

determine.subclone: Determine which clones are subclone in a single sample, also determine what clones are possible founder clones of the samples

Description

Usage

Arguments