scHiC_simulate: This function simulates single cells from 3D structure.

In Queen0044/HiCImpute: HiCImpute: An R Package Implementing "Bayesian Hierarchical Model for Identifying Structural Zeros and Enhancing Single-cell Hi-C Data"

This function simulates single cells from 3D structure.

Description

This function simulates single cells from 3D structure.

Usage

scHiC_simulate(
  data = str1,
  alpha_0,
  alpha_1,
  beta_l,
  beta_g,
  beta_m,
  gamma,
  eta,
  n_single
)

Arguments

data	3D coordinates of single cell.
alpha_0	Parameter that controls sequence depth of data.
alpha_1	Parameter that controls sequence depth of data.
beta_l	Parameter that controls effect size of covariate.
beta_g	Parameter that controls effect size of covariate.
beta_m	Parameter that controls effect size of covariate.
gamma	Quantile that is used as the threshold.
eta	Percent of structural zeros that are set to be common structural zeros among all single-cells.
n_single	Number of single cells to be generated.

Value

A list of underline true count, SZ positions, and generated single cells.

Examples

#Load 3d structure generated from SIMBA package
load("simba_3strs.rdata")
Set random seed
set.seed(1234)
#Generate 100 random type1 single cells
simudat <- scHiC_simulate(data=str1, alpha_0=5.6,alpha_1=-1, beta_l=0.9,beta_g=0.9,
beta_m=0.9,gamma=0.1,eta=0.8, n_single=10) 

Queen0044/HiCImpute documentation built on Oct. 9, 2022, 9:30 a.m.