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@@ -360,7 +360,11 @@ norm.scran <- function(x, vars=NULL, noscale=TRUE, min.mean=1){
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360
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360
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a <- SingleCellExperiment(assays=list(counts=a))
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361
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clusters <- quickCluster(a, min.mean=min.mean, min.size=50)
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a <- computeSumFactors(a, min.mean=min.mean, clusters=clusters)
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363
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- a <- scater::normalize(a)
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363
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+ if(is.null(logNormCounts)){
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364
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+ a <- scater::normalize(a)
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365
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+ }else{
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+ a <- logNormCounts(a)
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+ }
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364
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368
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if(is(x,"Seurat")){
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365
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369
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x <- SetAssayData(x, slot="data", new.data=logcounts(a))
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366
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370
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if(noscale){
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