ABSSeq (version 1.2.0)

normalFactors: Estimating size factors from the reads count table

Description

Function for esitmating size factors

Usage

normalFactors(object)

Arguments

object

an ABSDataSet object with element of 'counts' and 'normMethod', see the constructor functions ABSDataSet.

Value

sizeFactors to show it.

Details

Given a matrix of count data, this function esitmates the size factors by selected method. It provides four different methods for normalizing according to user-defined size factors, total reads, up quantile (75%) or DESeq (See estimateSizeFactorsForMatrix).

Examples

obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
obj <- normalFactors(obj)
sizeFactors(obj)