singleCellSimu {scDD} | R Documentation

## 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).

[Package scDD version 1.10.0 Index]