Description Usage Arguments Value Examples
The most recent version of scran depends on R > 3.4. I use scran 1.2.2, which depeneds on R.3.3.0. One difference that I have found so far is about SCESet - in the older version, the spike-in variable is a binary vector of yes/no, and in the newer version, the spike-in variable is a numeric vector specifying which genes is spike-in controls.
1 2 | normalize.scran(counts, control = list(save_modelFit = FALSE,
get_cell_clusters = FALSE, min.size = 50))
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counts |
Gene by sample expression count matrix (G by N). |
control |
List with control arguments, including
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libsize_factors
numeric vector of the scale factors for library size.
1 2 3 4 5 6 7 8 9 10 11 12 | ipsc_eset <- get(load(system.file("testdata", "HumanTungiPSC.rda", package = "ashbun")))
counts <- exprs(ipsc_eset)[sample(nrow(exprs(ipsc_eset)), ), ]
#---- generat simulated datasets
simdata_list <- simulationWrapper(counts, Nsim = 5, Nsample = 100, Ngene = 500)
#---- extract a single dataset as an example
#---- take pi0 = .9, the first simulated data
simdata <- simdata_list[[3]][[1]]
#---- normalize
output <- normalize.scran(simdata$counts)
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