calculateFPKM {scater} | R Documentation |
Calculate fragments per kilobase of exon per million reads mapped (FPKM) values from the feature-level counts.
calculateFPKM(x, lengths, ..., subset_row = NULL)
x |
A numeric matrix of counts where features are rows and cells are columns. Alternatively, a SummarizedExperiment or a SingleCellExperiment containing such counts. |
lengths |
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.
Aaron Lun, based on code by Davis McCarthy
calculateCPM
, for the initial calculation of CPM values.
example_sce <- mockSCE() eff_len <- runif(nrow(example_sce), 500, 2000) fout <- calculateFPKM(example_sce, eff_len) str(fout)