calculateFPKM {scuttle} | 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, ..., 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)

[Package scuttle version 1.4.0 Index]