degenes {NOISeq} | R Documentation

## Recovering differencially expressed features.

### Description

Recovering differencially expressed features for a given threshold from `noiseq` or `noiseqbio` output objects.

### Usage

    degenes(object, q = 0.95, M = NULL)

### Arguments

`object` | Object of class `Output`.
`q` | Value for the probability threshold (by default, 0.95).
`M` | String indicating if all differentially expressed features are to be returned or only up or down-regulated features. The possible values are: "up" (up-regulated in condition 1), "down" (down-regulated in condition 1), or NULL (all differentially expressed features).

### Value

A matrix containing the differencially expressed features, the statistics and the probability of differential expression.

### Author(s)

Sonia Tarazona

### References

Marioni, J.C. and Mason, C.E. and Mane, S.M. and Stephens, M. and Gilad, Y. (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research, 18: 1509–1517.

### See Also

`readData`, `noiseq`, `noiseqbio`.

### Examples

    ## Load the object mynoiseq generated by computing differential expression probability with noiseq() on Marioni's data:
    data(noiseq)

    ## Third, use degenes() function to extract differentially expressed features:
    mynoiseq.deg = degenes(mynoiseq, q = 0.8, M = NULL)

[Package NOISeq version 2.28.0 Index]