calculateFPKM: Calculate FPKMs

In LTLA/scuttle: Single-Cell RNA-Seq Analysis Utilities

Calculate FPKMs

Description

Calculate fragments per kilobase of exon per million reads mapped (FPKM) values from the feature-level counts.

Usage

calculateFPKM(x, lengths, ..., subset.row = NULL, subset_row = NULL)

Arguments

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 x.
...	Further arguments to pass to calculateCPM.
subset.row	A vector specifying the subset of rows of x for which to return a result.
subset_row	Soft-deprecated equivalent to the argument above.

Details

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.

Value

A numeric matrix of FPKM values with the same dimensions as x (unless subset.row is specified).

Author(s)

Aaron Lun, based on code by Davis McCarthy

See Also

calculateCPM, for the initial calculation of CPM values.

Examples

example_sce <- mockSCE()
eff_len <- runif(nrow(example_sce), 500, 2000)
fout <- calculateFPKM(example_sce, eff_len)
str(fout)

LTLA/scuttle documentation built on March 9, 2024, 11:16 a.m.