calculateTPM {scater} | R Documentation |
Calculate transcripts-per-million (TPM) values for expression from counts for a set of features.
calculateTPM(object, effective_length = NULL, calc_from = "counts")
object |
a |
effective_length |
vector of class |
calc_from |
character string indicating whether to compute TPM from
|
Matrix of TPM values.
data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info) tpm(example_sce) <- calculateTPM(example_sce, effective_length = 5e04, calc_from = "counts") ## calculate from FPKM fpkm(example_sce) <- calculateFPKM(example_sce, effective_length = 5e04, use.size.factors = FALSE) tpm(example_sce) <- calculateTPM(example_sce, effective_length = 5e04, calc_from = "fpkm")