calculateFPKM {scater} | R Documentation

## Calculate fragments per kilobase of exon per million reads mapped (FPKM)

### Description

Calculate fragments per kilobase of exon per million reads mapped (FPKM) values for expression from counts for a set of features.

### Usage

    calculateFPKM(object, effective_length, ..., subset_row = NULL)

### Arguments

`object` | A SingleCellExperiment object or a numeric matrix of counts.
`effective_length` | Numeric vector providing the effective length for each feature in `object`.
`...` | Further arguments to pass to `calculateCPM`.
`subset_row` | A vector specifying the subset of rows of `object` for which to return a result.

### Value

A numeric matrix of FPKM values.

### Examples

    data("sc_example_counts")
    data("sc_example_cell_info")
    example_sce <- SingleCellExperiment(
        list(counts = sc_example_counts),
        colData = sc_example_cell_info)

    eff_len <- runif(nrow(example_sce), 500, 2000)
    fout <- calculateFPKM(example_sce, eff_len, use_size_factors = FALSE)

[Package scater version 1.12.2 Index]