myCounts: Class myCounts

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

Description

This is the main class which contains the information needed to do the different analyses.

Extends

Class eSet (package 'Biobase').

Quick View

This object will contain the expression data and further information needed to do the exploratory analysis or the normalization such as the length, GC content, biotypes, chromosomes and positions for each feature.

Internally, the data is stored as follows:

As myCounts derives from eSet, we have used the slot assayData to store all the expression data, phenoData to store the factors with the conditions, featureData which will contain the variables Length, GCcontent, Biotype, Chromosome, Start Position, End Position for each feature. It has been used the slot experimentData derived from MIAME-class which will contain the type of replicates (biological replicates, technical replicates or no replicates at all).

Author(s)

Sonia Tarazona

See Also

If you need further information to know the methods that can be used, see eSet, AnnotatedDataFrame-class, MIAME-class.

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