maf_gmm_fit: Fits a gaussian mixture-of-alleles model

In lculibrk/Ploidetect: Ploidetect - Detection of tumour purity, aneuploidy, and copy number variation from whole genome sequnce data

Fits a gaussian mixture-of-alleles model

Description

maf_gmm_fit fits a gaussian mixture model for each possible copy number state to VAF data, computes the probability of each copy number and returns a matrix of probabilities for each copy number state

Usage

maf_gmm_fit(
  depth_data,
  vaf_data,
  chr_vec,
  means,
  variances,
  maf_variances,
  maxpeak,
  lowest = NA,
  ploidy = NA
)

Arguments

depth_data	input read depth data for all bins
vaf_data	input vaf data for all bins
chr_vec	vector of chromosomes for all bins
means	vector of mixture model means
variances	standard deviation for the mixture model
lowest	optional unless ploidy specified; what is the copy number of the first element of means?
ploidy	optional unless lowest specified; what is the most common copy number state?
vaf_variances	standard deviation for VAF values

Value

a matrix of likelihoods, where columns are copy number states and rows are input observations

lculibrk/Ploidetect documentation built on May 18, 2023, 5:53 p.m.