counts: Accessors for the 'counts' slot of a ABSDataSet object.

In ABSSeq: ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

Description

Accessors for the 'counts' slot of a ABSDataSet object, return a matrix

Usage

## S4 method for signature 'ABSDataSet'
counts(object,norm=FALSE)

## S4 replacement method for signature 'ABSDataSet,matrix'
counts(object)<-value

Arguments

object	a ABSDataSet object.
norm	logical indicating whether or not to normalize the counts before returning
value	an numeric matrix

Details

The counts slot holds the count data as a matrix of non-negative integer count values, rows and columns for genes and samples, respectively.

See Also

sFactors, normalFactors

Examples

data(simuN5)
obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
head(counts(obj))
counts(obj) <- matrix(1:50,nrow=5,ncol=10)
head(counts(obj))

ABSSeq documentation built on Nov. 8, 2020, 5:07 p.m.