User: luke.zappia

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luke.zappia30
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@_lazappi_
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Posts by luke.zappia

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Any pointers on simulating cell outliers?
... Cell outliers aren't part of the current model for the Splat simulation. I think your idea of having some groups with very small probabilities and relatively large DE factors is probably a good approach to try. Maybe something like: ``` sim <- splatSimulateGroups(group.prob = c(0.5, 0.4, 0.09, ...
written 4 weeks ago by luke.zappia30
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Any pointers on simulating cell outliers?
... Received via GitHub https://github.com/Oshlack/splatter/issues/47 I was wondering if it is possible to use Splatter to simulate cell outliers. In the documentation of Splatter, there are expression outlier parameters, but I did not find any specific information on cell outliers. Excuse me if I misse ...
simulation splatter written 4 weeks ago by luke.zappia30
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Answer: A: Accessing normalized counts
... The normcounts function is a shortcut for accessing an assay named normcounts. Neither the simulation functions in Splatter or the normalise function (which is in the scater package) create this assay, which is why you are seeing the error. You can see what assays are present using assayNames(sim.pa ...
written 9 weeks ago by luke.zappia30
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Accessing normalized counts
... Received via GitHub https://github.com/Oshlack/splatter/issues/42 When I try to access the normalized counts from a path simulation, I get the following error: Error in assay(object, i = exprs_values) : 'assay(<SingleCellExperiment>, i="character", ...)' invalid subscript 'i' 'i' not in nam ...
scater splatter singlecellexperiment written 9 weeks ago by luke.zappia30
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Comment: C: splatter simulating paths
... Hi @nikolaspapadop That is correct. I like your diagram, I might look at including that in the help page for the function. ...
written 9 weeks ago by luke.zappia30
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Answer: A: Simulating paths returns identical values
... When you run View(assay(sim.paths)) you are being shown the first matrix in the assays slot which contains some intermediate values. To see the counts that have been produced you should use counts(sim.paths) or View(assay(sim.paths, "counts")). A simple PCA plot coloured by the step along the path c ...
written 10 weeks ago by luke.zappia30
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Simulating paths returns identical values
... Question received via GitHub https://github.com/Oshlack/splatter/issues/41 I was trying to simulate a differentiation, and followed the instructions for paths in Introduction to Splatter. However, when I then looked at the data with assay(sim.paths), I was greeted by a matrix where all columns (cell ...
splatter written 10 weeks ago by luke.zappia30
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Answer: A: Splatter: How to simulate cells in different groups and different path at the sa
... At the moment the ideas of groups and paths are separate, so it is not possible to simulate them at the same time. It's a little had to say without knowing more about exactly what you want to simulate but you might be able to simulate something like what you want by playing around with the path par ...
written 7 months ago by luke.zappia30
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Splatter: How to simulate cells in different groups and different path at the same time?
... Received as GitHub issue https://github.com/Oshlack/splatter/issues/28 Hello, I found that I would simulate groups use splatSimulateGroups() and use splatSimulatePaths() to simulate the path, how could I simulate them at the same time? ...
splatter written 7 months ago by luke.zappia30
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Answer: A: Control group size
... 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 an ...
written 7 months ago by luke.zappia30

Latest awards to luke.zappia

Scholar 12 months ago, created an answer that has been accepted. For A: Accessing normalized counts
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Accessing normalized counts

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