simRNAseq: Simulate RNA-seq count data

In PROPER: PROspective Power Evaluation for RNAseq

Description

This function generate simulated RNA-seq count data for a two-group comparison design. It takes an object for simulation option (return object from 'RNAseq.SimOptions.2grp' function, and sample sizes (replicates in each condition, then generate a matrix of counts.

Usage

simRNAseq(simOptions, n1, n2)

Arguments

simOptions	An object for simulation option. This should be the return object from 'RNAseq.SimOptions.2grp' function.
n1, n2	Sample size in two treatment groups.

Details

The count data are generated based a negative binomial (NB) distribution. Parameters for NB are provided in the input object.

Value

A list with following fields:

counts	A matrix of dimension ngenes x (n1+n2). Each row is for a gene, each column is for a sample. Columns 1 to n1 are for the first condition. The rest columns are for the other condition.
designs	A vector/matrix representing the experimental designs. In a two-group comparison, it's a simple 0/1 vector.
DEid	The ID (row index) for true DE genes.
simOptions	The simulation option object. This is exactly the same as the input simOptions.

Author(s)

Hao Wu <[e-mail]>

See Also

RNAseq.SimOptions.2grp, runSims

Examples

simOptions = RNAseq.SimOptions.2grp()
data = simRNAseq(simOptions, n1=3, n2=3)
names(data)

Example output

[1] "counts"     "designs"    "DEid"       "simOptions"

PROPER documentation built on Nov. 8, 2020, 6:31 p.m.