calculateFPKM {scater} | R Documentation |
Calculate fragments per kilobase of exon per million reads mapped (FPKM) values for expression from counts for a set of features.
calculateFPKM(object, effective_length, ..., subset_row = NULL)
object |
A SingleCellExperiment object or a numeric matrix of counts. |
effective_length |
Numeric vector providing the effective length for each feature in |
... |
Further arguments to pass to |
subset_row |
A vector specifying the subset of rows of |
A numeric matrix of FPKM values.
data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( list(counts = sc_example_counts), colData = sc_example_cell_info) eff_len <- runif(nrow(example_sce), 500, 2000) fout <- calculateFPKM(example_sce, eff_len, use_size_factors = FALSE)