Lab 3 - Run SCTransform

[pontushojer]

For normalization we currently load a RDS file se that is too large to fit on github. This is a bit annoying as we need to provide this file separately. The rationale behind this was that SCTransfrom took a long time to run. However I did a test just now and it finished in ~6 s.

code

{r}
startTime <- Sys.time()

SCTransform(se, verbose=FALSE)

endTime <- Sys.time()
print(endTime - startTime)

output

An object of class Seurat 
35712 features across 864 samples within 2 assays 
Active assay: SCT (16777 features, 3000 variable features)
 1 other assay present: RNA
Time difference of 5.701049 secs

This was using version 0.3.5 on Posit cloud (6Gb RAM). Seems its a lot faster these days, thus we could safely run it as a part of the lab and skip loading the data/se file.