singleCellSimu: singleCellSimu

In kdkorthauer/scDD: Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

singleCellSimu

Description

Called by simulateSet to simulate a specified number of genes from one DD category at a time.

Usage

singleCellSimu(Dataset1, Method, index, FC, modeFC, DP, Validation = FALSE,
  numGenes = 1000, numDE = 100, numSamples = 100,
  generateZero = c("empirical", "simulated", "constant"),
  constantZero = NULL, varInflation = NULL)

Arguments

Dataset1	Numeric matrix of expression values with genes in rows and samples in columns.
Method	Type of simulation should choose from "DE" "DP" "DM" "DB"
index	Reasonable set of genes for simulation
FC	Fold Change values for DE Simulation
modeFC	Vector of values to use for fold changes between modes for DP, DM, and DB.
DP	Differetial Proportion vector
Validation	Show Validation plots or not
numGenes	numeric value for the number of genes to simulate
numDE	numeric value for the number of genes that will differ between two conditions
numSamples	numeric value for the number of samples in each condition to simulate
generateZero	Specification of how to generate the zero values. If "empirical" (default), the observed proportion of zeroes in each gene is used for the simuated data, and the nonzeroes are simulated from a truncated negative binomial distribution. If "simulated", all values are simulated out of a negative binomial distribution, includling the zeroes. If "constant", then each gene has a fixed proportion of zeroes equal to constantZero.
constantZero	Numeric value between 0 and 1 that indicates the fixed proportion of zeroes for every gene. Ignored if generateZero method is not equal to "constant".
varInflation	Optional numeric vector with one element for each condition that corresponds to the multiplicative variance inflation factor to use when simulating data. Useful for sensitivity studies to assess the impact of confounding effects on differential variance across conditions. Currently assumes all samples within a condition are subject to the same variance inflation factor.

Value

Simulated_Data A list object where the first element contains a matrix of the simulated dataset, the second element contains the DEIndex, and the third element contains the fold change (between two conditions for DE, between two modes for DP, DM, and DB).

kdkorthauer/scDD documentation built on March 27, 2022, 5:11 a.m.