change values on Differential Expression parameters
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jp3770 • 0
@jp3770-22142
Last seen 2.0 years ago

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 • 215 views
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luke.zappia ▴ 50
@lukezappia-11973
Last seen 7 months ago

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.

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