Question: change values on Differential Expression parameters
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gravatar for jp3770
5 weeks ago by
jp37700
jp37700 wrote:

Hello! I am trying to simulate single-cell data, generating different populations. I am wondering if, and how, I can change values of the Differential expression paramters (% of differential expressed genes and the difference in expression). In newSplatParams() We have Diff expr: [Probability] [Down Prob] [Location] [Scale]

But I do not know how to change them. THank you for your help in advance! J

splatter • 68 views
ADD COMMENTlink modified 4 weeks ago by luke.zappia50 • written 5 weeks ago by jp37700
Answer: change values on Differential Expression parameters
0
gravatar for luke.zappia
4 weeks ago by
luke.zappia50
luke.zappia50 wrote:

Hi @jp3770

Parameters can be set in few ways. These are examples for the Splat simulation but the same is true for the other models.

  • When creating a parameters object - params <- newSplatParams(nGenes = 100)
  • Updating an existing parameters object - params <- setParam(params, "nGenes", 100)
  • Supplied to the simulation function - sim <- splatSimulate(nGenes = 100)

The differential expression parameters you asked about are named de.prob, de.downProb, de.facLoc and de.facScale. You can see more about all the parameters for the Splat simulation by looking at the help file for the SplatParams object with ?SplatParams.

ADD COMMENTlink written 4 weeks ago by luke.zappia50
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