calculateFPKM {scater}R Documentation

Calculate FPKMs

Description

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

Usage

calculateFPKM(x, lengths, effective_length = 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.

effective_length

Deprecated, same as lengths.

...

Further arguments to pass to calculateCPM.

subset_row

A vector specifying the subset of rows of x for which to return a result.

Value

A numeric matrix of FPKM values.

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)

[Package scater version 1.14.0 Index]