calculateCPM {scater} | R Documentation |
Calculate count-per-million (CPM) values from the count data.
calculateCPM(object, use.size.factors = TRUE)
object |
an |
use.size.factors |
a logical scalar specifying whether the size factors should be used to construct effective library sizes, or if the library size should be directly defined as the sum of counts for each cell. |
Matrix of CPM values.
data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info) cpm(example_sce) <- calculateCPM(example_sce, use.size.factors = FALSE)