makeFCMatrix {TCC} | R Documentation

## Generate the fold change matrix for simulating count data

### Description

Generate the fold change matrix for simulating count data under the Gammma distribution

### Usage

    makeFCMatrix(Ngene = 10000, PDEG = 0.20, DEG.assign = NULL,
                 replicates = NULL, fc.params = NULL)

### Arguments

`Ngene` | numeric scalar specifying the number of genes.
`PDEG` | numeric scalar specifying the proportion of differentially expressed genes (DEGs).
`DEG.assign` | numeric vector specifying the proportion of DEGs up- or down-regulated in individual groups to be compared. The number of elements should be the same as that of `replicates` if `replicates` is specified. The indication of `replicates` means a single-factor experimental design.
`replicates` | numeric vector indicating the numbers of (biological) replicates for individual groups compared. Ignored if `group` is specified.
`fc.params` | foldchanges of DEGs are randomly sampled from f + Γ(a, b) where a is a shape and b is a scale of Gamma distribution. The default values are f = 1.2, a = 2, and b = 0.5

### Details

`makeFCMatrix` function is a function for generating the foldchanges of DEGs. The foldchanges are randomly sampled from f + Γ(a, b) where a is a shape and b is a scale of Gamma distribution.

### Value

matrix

### Examples

    fc.matrix <- makeFCMatrix()

[Package TCC version 1.28.0 Index]