ABSSeq (version 1.8.0)

normalFactors: Estimating size factors from the reads count table

Description

Function for esitmating size factors

Usage

normalFactors(object)

Arguments

object

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

Value

a ABSDataSet object with the estimates size factors, one element per column. Use the sFactors to show it.

Details

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

Examples

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