calculateFPKM: Calculate fragments per kilobase of exon per million reads...

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

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 SCESet 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_sceset <- newSCESet(countData = sc_example_counts)
effective_length <- rep(1000, 2000)
fpkm(example_sceset) <- calculateFPKM(example_sceset, effective_length)

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.