enumerate.clones: Enumerate all possible clonal structures for a single sample,...

In hdng/clonevol: Clonal ordering and visualization

Description

Enumerate all possible clonal structures for a single sample using monoclonal (ie. the primary tumor is originated from a single cancer cell) or polyclonal model (ie. the primary tumor can originate from multi cancer cells)

Usage

enumerate.clones (v, sample, variants=NULL, subclonal.test.method='bootstrap'
, boot=NULL, p.value.cutoff=0.1)

Arguments

v:	a data frame output of make.clonal.data.frame function

Details

This function return a list of data frames. Each data frame represents a clonal structure, similar to the output format of make.clonal.data.frame output but now have 'parent' column identified indicating the parent clone, and other columns (free, occupied) which can be used to calculate cellular fraction and plotting. The root clone has parent = -1, clones that have VAF=0 will have parent = NA

hdng/clonevol documentation built on May 17, 2019, 3:19 p.m.