degenes: Recovering differencially expressed features.

In SoniaTC/NOISeq: Exploratory analysis and differential expression for RNA-seq data

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)

SoniaTC/NOISeq documentation built on July 28, 2020, 6:31 p.m.