4.3 Filter

Finally, let’s filter the data to remove spots with very high mitochondrial content. You can filter the data based on many different parameters, it’s up to you to test and decide what you think is best for the analysis you want to perform.

# Keep spots with less than 30% mitochondrial content
se.subset <- SubsetSTData(se, expression = pct.mt < 40)

cat("Spots removed: ", ncol(se) - ncol(se.subset), "\n")

## Spots removed:  14