TCC (version 1.12.1)

makeFCMatrix: 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 $f + \Gamma(a, b)$ where $a$ is a shape and $b$ is a scale of Gamma distribution. The default values are $f = 1.2$, $a = 2$, and $b = 0.5$

Value

Details

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

Examples

fc.matrix <- makeFCMatrix()