Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/calculateFPKM.R
Calculate fragments per kilobase of exon per million reads mapped (FPKM) values from the feature-level counts.
1 | calculateFPKM(x, lengths, ..., subset.row = NULL, 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 |
subset_row |
Soft-deprecated equivalent to the argument above. |
FPKMs are computed by dividing the CPMs by the effective length of each gene in kilobases. For RNA-seq datasets, the effective length is best set to the sum of lengths of all exons; for nucleus sequencing datasets, the effective length may instead be the entire width of the gene body.
A numeric matrix of FPKM values with the same dimensions as x
(unless subset.row
is specified).
Aaron Lun, based on code by Davis McCarthy
calculateCPM
, for the initial calculation of CPM values.
1 2 3 4 | example_sce <- mockSCE()
eff_len <- runif(nrow(example_sce), 500, 2000)
fout <- calculateFPKM(example_sce, eff_len)
str(fout)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.