makeSimulatedData: Make simulated data for airpart

In Wancen/airpart: Differential cell-type-specific allelic imbalance

Make simulated data for airpart

Description

Make simulated data for airpart

Usage

makeSimulatedData(
  mu1 = 2,
  mu2 = 10,
  nct = 4,
  n = 30,
  ngenecl = 50,
  theta = 20,
  ncl = 3,
  p.vec = rep(c(0.2, 0.8, 0.5, 0.5, 0.7, 0.9), each = 2),
  totalClusters = FALSE
)

Arguments

mu1	low count (typical of "noisy" ratio estimates)
mu2	high count
nct	number of cell types
n	number of cells per cell type
ngenecl	number of genes per cluster
theta	overdispersion parameter (higher is closer to binomial)
ncl	number of gene cluster
p.vec	the allelic ratio vector which follows gene cluster order. (length is nct * ncl)
totalClusters	logical, whether cell types should cluster by total count

Value

SingleCellExperiment with the following elements as assays

• a1 allelic count matrix for the numerator/effect allele

• a2 allelic count matrix for the denominator/non-effect allele

• true.ratio a matrix of the true probabilities (allelic ratios) for the cell types

Also x in the colData is a vector of annotated cell types in the same order as cells in count matrix

Examples

library(SummarizedExperiment)
sce <- makeSimulatedData()
assayNames(sce)

Wancen/airpart documentation built on March 12, 2023, 11:53 a.m.