Calculate QC metrics

To remove problematic cells and genes, we want to calculate quality control metrics using the calculateQCMetrics() function from the package scater, which is a useful package for quality control and analysis of single-cell data. These metrics will help us filter out low quality genes and cells.

Remember that to identify problematic cells, experimentalists sometimes use synthetic spike-in RNAs as positive controls. The spike-in RNA names start with "ERCC", and are already stored as isSpike(sce, "ERCC").

Load the library scater.
Use the calculateQCMetrics() function to calculate quality control (QC) metrics and assign it back to sce. A list of the QC metrics calculated by this function is available in the documentation of the function (type ?calculateQCMetrics in the console to access the help).
After calculateQCMetrics() has been applied to sce, columns are added to colData(sce). Explore colData(sce).

Take Hint (-30 XP)

Exercise

Calculate QC metrics

Instructions