setupCurves: Plot dilution curves at given multiplicities

In ndbrown6/CNtu: Copy Number tree utilities

Plot dilution curves at given multiplicities

Description

Plots dilution curves of expected VAFs at all multiplicites i.e. 2/1, 2/2, 3/1, 3/2, etc given contamination with normal cells harboring two non mutated copies

Usage

setupCurves(nqt, col, lty, f_hat, qt, sq)

Arguments

nqt	integer maximum number of total copies
col	character vector of colors for the different copy numbers where ||col|| = nqt
lty	numeric vector of line types for the different multiplicities where ||lty|| = nqt
f_hat	optional numeric vector of observed VAFs where f_hat = 0 … 1
qt	optional integer vector total copy numbers where ||qt|| = ||f_hat||
sq	optional integer vector of number of mutated copies where ||sq|| = ||f_hat||

Value

None

Note

If f_hat, qt and sq are provided, the function cellularFraction(...) is called to compute the maximum likelihood of cellular fractions. These are displayed as a scatter plot above the dilution curves. For clarity, user should not attempt to go beyond nqt = 3 and similarly remove points in f_hat, qt and sq where qt>3.

Author(s)

David Brown
[e-mail]

ndbrown6/CNtu documentation built on March 16, 2023, 1:01 a.m.