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]