singleCellSimu: singleCellSimu

Description Usage Arguments Value

View source: R/Single_Cell_Simu.R

Description

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

Usage

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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).


scDD documentation built on Nov. 8, 2020, 7:10 p.m.