scater (version 1.0.4)

calculateFPKM: 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)

Arguments

object

an SCESet object

effective_length

vector of class "numeric" providing the effective length for each feature in the SCESet object

Value

Matrix of FPKM values.

Examples

data("sc_example_counts")
data("sc_example_cell_info")
example_sceset <- newSCESet(countData = sc_example_counts)
effective_length <- rep(1000, 2000)
fpkm(example_sceset) <- calculateFPKM(example_sceset, effective_length)