counts {OUTRIDER} | R Documentation

## 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]

[Package OUTRIDER version 1.12.0 Index]