estimate.ccf

clonal evolution of a sample data frame

sample:

row of vx where clone needs to be estimated

boot:

minimum cluster vaf to consider non-zero

min.cluster.vaf:

alpha:

if subclonal.test was run already, provide the return object, if NULL
subclonal.test will be run
Return vx with additionally annotated columns related to CCF

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.

estimate.ccf: Calculate CI of CCF, pvals, etc.

Description

Usage

Arguments