normalize,Asset-method {Allspice}

Sample normalization

Description

Adjust scale differences between samples.

Usage

normalize(obj, dat)

Arguments

obj

An object of the class Asset.

dat

A matrix that containts variables as rows and samples as columns.

Details

The normalization pipeline comprises three steps. First, variable names are checked against the internal nomenclature and converted to the internal naming scheme where necessary (see nomenclature()). Second, variables that are present in the internal normalization reference are imputed with reference values if not available in the data. Third, the data are normalized according to the DESeq2 algortihm (Love MI, Huber W & Anders S, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol 15, 550, 2014).

Value

Returns a matrix in the same format as the input.

Examples

# Import ALL subtyping asset.
base <- system.file(package = "Allspice")
folder <- file.path(base, "subtypes")
a <- asset(folder)

# Simulated data.
simu <- bcellALL(5)

# Normalize RNA read counts.
expres <- normalize(a, dat = simu$counts)
print(head(simu$counts))
print(head(expres))