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 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

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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)

scater documentation built on May 31, 2017, 3:08 p.m.

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