donor_read_simulator: Reads simulator for donor identification

In PMBio/cardelino: Clone Identification from Single Cell Data

Reads simulator for donor identification

Description

Reads simulator for donor identification

Usage

donor_read_simulator(
  GT,
  D_seed,
  sample_variants = FALSE,
  donor_size = NULL,
  beta_shapes = NULL,
  n_cell = 5000,
  doublet_rate = NULL
)

Arguments

GT	Variant-by-donor matrix for genotypes
D_seed	Variant-by-cell matrix for read coverage for generating depth, which be row sample and column sample both with replacement
sample_variants	logical(1), if TRUE, sample variants with replacement to the same size, otherwise not
donor_size	Vector of float for the fractions of each donor; default NULL means uniform
beta_shapes	A 3-by-2 matrix of beta parameters for genotypes: 0, 1, and 2; default NULL means matrix(c(0.2, 0.5, 99.8, 99.8, 0.5, 0.2), nrow = 3)
n_cell	An integer for number of total cells
doublet_rate	A float from 0 to 1 for doublet rate; default NULL means rate n_cell / 100000

Value

A list of various components of the simulated dataset.

PMBio/cardelino documentation built on Nov. 21, 2022, 4:52 a.m.