SimSetup: DEA options for RNA-seq count simulations in two-group...

In bvieth/powsim: Power Simulations

Description

This function adds user provided options for simulating RNA-seq data to RNAseq.SimSetup object. The resulting output list object is the input for simulateDE function.

Usage

SimSetup(desetup, params, size.factors='equal')

Arguments

desetup	The RNAseq simulation parameters created by DESetup.
params	The negative binomial parameters for simulations. This can be: (1) The output of estimateNBParam. (2) The output of insilicoNBParam. (3) A string specifying the name of precalculated estimates, see details.
size.factors	Size factors representing sample-specific differences/biases in expected mean values of the NB distribution: "equal" or "given". The default is "equal", i.e. equal size factor of 1. If the user defines it as given, the size factors are sampled from the size factors provided by the output of estimateNBParam or insilicoNBParam.

Value

A list with the following entries:

desetup	The RNAseq simulation parameters.
params	The negative binomial parameters for simulations.
size.factors	Size factor definition: "equal" or "given"

Author(s)

Beate Vieth

Examples

## Not run: 
desettings <- DESetup(ngenes=10000,
nsims=25, p.DE=0.2,
LFC=function(x) sample(c(-1,1), size=x,replace=TRUE)*rgamma(x, 3, 3))
simsettings <- SimSetup(desetup=desettings,
params=estparam, size.factors='equal')

## End(Not run)

bvieth/powsim documentation built on May 13, 2019, 9:04 a.m.