sim {sSeq} | R Documentation

## Generating Simulated Data

### Description

This function is used to approximate the real experiment and to generate simulated counts table based on Negative Binomial distribution.

### Usage

    sim(ngenes, true_mean1, conds,
      alpha = function(m) {rep(0.1, length(m))},
      mean_DE = 0, sd_DE = 2, s0 = NULL, s0_mean = 2, s0_sd = 3,
      true_isDE_proportion = 0.3)

### Arguments

`ngenes` | The total number of genes or rows in the simulated counts table.
`true_mean1` | The expected gene expression (μ_{g}) in a library or a sample. The length of this vector equals ‘ngenes’. It can generated from either random distributions or averages of counts table from a real experiment.
`conds` | A vector of characters representing the two conditions (or two groups). It must be matchable to the columns in countsTable, e.g., c("A", "A", "B", "B") matches to a countsTable that has four columns (or samples) in which the first two columns are samples under condition A and the last two columns are samples under condition B.
`alpha` | A function used to generate the true dispersion values. The default function generates a constant 0.1 for all the genes. It can also be a function specifying the dependence between dispersion and mean.
`mean_DE` | A true mean value of ε in μ_{gB}=μ_{g}/exp(ε) where ε follows a Normal distribution.
`sd_DE` | A true standard deviation of ε in μ_{gB}=εμ_{g} where ε follows a Normal distribution.
`s0` | The true size factors for samples. The length of this vector equals to the length of the vector ‘conds’.
`s0_mean` | If the true size factors for samples are not defined for ‘s0’, then the true size factors are assumed to follow a Normal distribution with mean as the value for ‘s0_mean’.
`s0_sd` | If the true size factors for samples are not defined for ‘s0’, then the true size factors are assumed to follow a Normal distribution with standard deviation as the value for ‘s0_sd’.
`true_isDE_proportion` | The proportion of genes that are truly different. The default value is 0.3.

### Value

The function outputs a list including the simulated counts table, a vector with TRUE of FALSE values indicating the truly differentiating genes, the true mean values, the true variance values, and the true dispersion values.

### Note

We acknowledge Dr. Simon Anders since he provided the details for simulation in the manual of DESeq package.

### References

Yu, D., Huber, W. and Vitek O. (2013). Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size. Bioinformatics.

### Examples

    ng = 10000;
    sim1 <- sim(ngenes=ng, conds=c("A","A","B","B"),
       true_mean1=round(rexp(ng, rate=1/200)), alpha=function(m){1/(m+100)},
       mean_DE=2, sd_DE=1, s0=runif(4, 0, 2) );
    true_isDE <- sim1$true_isDE;
    countsTable <- sim1$countsTable;

[Package sSeq version 1.28.0 Index]