counts: Accessors for the 'counts' slot of an OutriderDataSet object.

In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

Accessors for the 'counts' slot of an OutriderDataSet object.

Description

The counts slot holds the count data as a matrix of non-negative integer count values, one row for each observational unit (eg.: gene), and one column for each sample.

Usage

## S4 method for signature 'OutriderDataSet'
counts(object, normalized = FALSE, minE = 0.5, ...)

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

Arguments

object	An OutriderDataSet object
normalized	TRUE/FALSE whether counts should be normalized
minE	The minimal expected count, defaults to 0.5, to be used in computing the expected log geom mean.
...	Further arguments are passed on to the underlying assay function
value	An integer matrix containing the counts

Details

By default this function returns the raw counts. If conrol factors are computed or provided the normalized counts can be returned using normalized = TRUE. The offset parameter can be used to add a pseudocount to the count before dividing by the normalization. This can be usefull when the log(counts) are computed and in case the controll values are in the same oder of magnited as the counts.

Value

A matrix containing the counts

See Also

sizeFactors, normalizationFactors

Examples

ods <- makeExampleOutriderDataSet()
counts(ods)[1:10,1:10]

ods <- estimateSizeFactors(ods)
counts(ods, normalized=TRUE)[1:10,1:10]

gagneurlab/OUTRIDER documentation built on April 29, 2024, 2:22 a.m.