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Exercise

Explore Tung dataset

Let's take a first look at the Tung dataset. We first want to remove genes that have only zero counts since we'll never get information from these genes. We then want to identify the ERCC genes to be able to use them in the next exercises.

You'll experiment with using counts() and isSpike() here, and the data is stored in the SingleCellExperiment object sce.

Instructions
100 XP

  • Use counts() on the SCE object to create a Boolean matrix nonZero that has values TRUE if a count for a particular cell/gene combination is nonzero.

  • Use rowSums() to find the rows (i.e.genes) of nonZero which have at least one non-zero count, and assign the result to keep.

  • Explore the new SCE sce_2 that contains only genes with nonzero counts.

  • Use the grepl() function to detect the rownames of sce_2 that start with ERCC.Assign this to spiked-in ERCC genes in sce_2.