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

Description Usage Arguments Value Examples

View source: R/calculate-expression.R

Description

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

Usage

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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

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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)

scater documentation built on Dec. 5, 2017, 2 a.m.