User: luke.zappia

luke.zappia50
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Posts by luke.zappia

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... All the intermediate parameters are stored in various slots of the SingleCellExperiment object that is returned, I suggest you take a look at these to see what will be useful for you. To find which genes are DE have a look at the DEFacGroupX columns in rowData(sim). These can be considered as ...
written 4 months ago by luke.zappia50
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... Hi chenxofhit I'm not quite sure I understand the design you want but here is an example that might get us started. r library(splatter) sim <- splatSimulate(nGenes = 5000, batchCells = c(250, 250), group.prob = c(0.5, 0.5), de.p ...
written 4 months ago by luke.zappia50
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... Hi Brian Thanks for giving Splatter a go. I'm going to assume you are using the Splat simulation but you might want to check out some of the others depending on your use case. The Splat estimation process fits distributions to the data and there is no direct connection between an individual gene i ...
written 7 months ago by luke.zappia50
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... 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 13 months ago by luke.zappia50
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... 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 ...
written 13 months ago by luke.zappia50
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... 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 14 months ago by luke.zappia50
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... 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 ...
written 14 months ago by luke.zappia50
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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 14 months ago by luke.zappia50
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... 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 14 months ago by luke.zappia50
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... 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 ...
written 14 months ago by luke.zappia50

Latest awards to luke.zappia

Scholar 2.0 years ago, created an answer that has been accepted. For A: Accessing normalized counts
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Accessing normalized counts

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