Control group size
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luke.zappia ▴ 50
@lukezappia-11973
Last seen 7 months ago

Originally posted on GitHub https://github.com/Oshlack/splatter/issues/27

I have been using the following code to simulate different groups of single cells":

splatter_sim_1 <- splatSimulateGroups(groupCells = c(100, 100, 100, 100, 100), nGenes = 500, de.prob = c(0.05, 0.05, 0.05, 0.05, 0.05), de.facLoc = 3, de.facScale = 0, dropout.present = TRUE, seed = 1)

Since the update to R version 3.4 and the newest Bioconductor version this code gives an error:

Error in checkSlotAssignment(object, name, value) : ‘groupCells’ is not a slot in class “SplatParams”

I am not sure how to write code in the new version, which simulates different groups. Can someone help me?

splatter • 569 views
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Entering edit mode
luke.zappia ▴ 50
@lukezappia-11973
Last seen 7 months ago

Some of the parameters have changed in the latest release. You now want to use the batchCells and group.prob parameters. For example splatSimulateGroups(batchCells = 1000, group.prob(0.5, 0.3, 0.2)) would give you 1000 cells in three groups with probabilities of 0.5, 0.3 and 0.2. See the vignette and documentation for more details.

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