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 1.10.1 Index]