getDifferences {FourCSeq} | R Documentation

## Detect differences

### Description

`getDifferences` detects differences in the interaction frequencies between different conditions. For each viewpoint all possible combinations of conditions are tested using the `DESeq2` package.

### Usage

    getDifferences(object, referenceCondition = NULL, fitNormFactors = TRUE)

### Arguments

`object` | A `FourC` object.
`referenceCondition` | Reference condition to be used for testing.
`fitNormFactors` | Defines if the distance dependency should be used to estimate normalizationFactors. Default is `TRUE`.

### Value

Returns an updated `FourC` object that contains the results and information from the differential testing. Normalization factors are added to the assays slot.

### Author(s)

Felix A. Klein, felix.klein@embl.de

### See Also

`FourC`, `getZScores`, `estimateDispersions`, `nbinomWaldTest`

### Examples

    data(fcf, package="FourCSeq")

    fcf <- getDifferences(fcf, referenceCondition="WE_68h")

    results <- getAllResults(fcf)
    results

[Package FourCSeq version 1.20.0 Index]