normalize_counts: Normalize raw read counts of RNA-seq experiments

In szymczak-lab/QCnormSE: Quality Control of Normalized Gene Expression Data

Normalize raw read counts of RNA-seq experiments

Description

Generates normalized read counts of RNA-seq data sets using several functions provided in the Bioconductor package edgeR.

Usage

normalize_counts(
  se,
  assay = 1,
  method = "tmm",
  col.gene.length = "bp_length",
  log = TRUE,
  prior.count = 2
)

Arguments

se	RangedSummarizedExperiment-class object
assay	Character or integer. Name or number of assay containing raw read counts.
method	Method to use for normalizing: "tmm" (default), "cpm", "rpkm".
col.gene.length	Character or integer. Name or number of column in rowData containing gene length information. Only used by method "rpkm".
log	Logical. Should log2 transformed values be returned?
prior.count	Numeric. Average count to be added to each observation to avoid taking log of zero.

Value

RangedSummarizedExperiment-class object with normalized read counts in additional assay called <assay>.norm.

Examples

library(recount)
data("rse_gene_SRP009615")

rse_gene_SRP009615 = normalize_counts(se = rse_gene_SRP009615,
                                      method = "tmm")

szymczak-lab/QCnormSE documentation built on March 25, 2023, 1:05 p.m.