normBy: Normalization by edgeR, DESeq2 or RUVSeq

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Normalization by edgeR, DESeq2 or RUVSeq

Description

Normalization by multiple known methods

Usage

normBy(counts, method = c("edgeR", "DESeq2", "RUVs", "fpkm", "vsn"), ...)

Arguments

counts	Output of countReads
method	Character(1L) to indicate the method for normalization.
...	parameters will be passed to normByRUVs or getFPKM

Value

Normalized counts list

Examples

path <- system.file("extdata", package="ribosomeProfilingQC")
cnts <- readRDS(file.path(path, "cnts.rds"))
norm <- normBy(cnts, method = 'edgeR')
norm2 <- normBy(cnts, method = 'DESeq2')
norm3 <- normBy(cnts, 'vsn')

jianhong/ribosomeProfilingQC documentation built on Nov. 3, 2024, 6:33 p.m.