emcncf2: EM estimate of copy number and cellular fraction with clonal...

In rptashkin/facets2n: Cellular Faction and Copy Numbers from Tumor Sequencing

EM estimate of copy number and cellular fraction with clonal and subclonal cluster structure

Description

Uses genotype mixture model to estimate copy number, cellular fraction, and subclonal structures. \ Uses estimates based on the cnlr.median and mafR as initial values for the EM iteration.

Usage

emcncf2(
  x,
  trace = FALSE,
  unif = FALSE,
  min.nhet = 15,
  maxiter = 10,
  difcf = 0.05,
  maxk = 5,
  eps = 0.001
)

Arguments

x	(list) the output from procSample. This function uses the elements jointseg, out and dipLogR from the output.
trace	(logical) flag to print the EM criteria at every step
unif	(logical) random EM start values of cellular fractions instead of clusteredcncf values
min.nhet	(numeric) minimum number of heterozygote snps in a segment used to call minor cn
maxiter	(numeric) maximum number of EM iterations
difcf	(numeric) the minimal difference between segment cluster specific cellular fraction estimate and clonally constrained estimate for declaring candidate subclonal events
maxk	(numeric) maximum number of clonal and subclonal clusters allowed for the fit
eps	(numeric) the convergence threshold

Value

A list containing:

loglik	loglikelihood value of the fitted model
purity	fraction tumor cells in the tumor sample
ploidy	average total copy number of the tumor cells
dipLogR	estimated logR value of diploid segments
cncf	dataframe consisting of the columns of segmentation output as well as cellular fraction (cf), total (tcn) and lesser (lcn) copy number of each segment and their em counterpart (with .em suffix), and a clonal.cluster indicater with clonal.cluster=1 indicating the clonal cluster and a higher number (2,3, etc..) indicating subclonal clusters.

rptashkin/facets2n documentation built on May 11, 2022, 1:34 p.m.