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, use.size.factors = TRUE)

### Arguments

`object` | an `SingleCellExperiment` object
`effective_length` | vector of class `"numeric"` providing the effective length for each feature in the `SCESet` object
`use.size.factors` | a logical scalar, see `calculateCPM`

### Value

Matrix of FPKM values.

### Examples

    data("sc_example_counts")
    data("sc_example_cell_info")
    example_sce <- SingleCellExperiment(
    assays = list(counts = sc_example_counts), colData = sc_example_cell_info)
    effective_length <- rep(1000, 2000)
    fpkm(example_sce) <- calculateFPKM(example_sce, effective_length,
    use.size.factors = FALSE)

[Package scater version 1.6.3 Index]