CountDataSet-class {DESeq} | R Documentation

## Class "CountDataSet" – a container for count data from HTS experiments

### Description

This is the main class for the present package.

### Objects from the Class

Objects should be created with calls to `newCountDataSet` (q.v.).

### Extends

Class `eSet` (package 'Biobase'), directly. Class `VersionedBiobase` (package 'Biobase'), by class "eSet", distance 2. Class `Versioned` (package 'Biobase'), by class "eSet", distance 3.

### Note

Note: This is a summary for reference. For an explanation of the actual usage, see the vignette.

A CountDataSet object stores counts from an HTS data set and offers further slots which are populated during the analysis.

After creation with `newCountDataSet`, a CountDataSet typically contains a count table, i.e., a matrix of integer data, that is accessible with the accessor function `counts`. Each row of the matrix corresponds to a gene (or binding region, or the like), and each colum to an experimental sample. The experimental conditions of the samples are stored in a factor (with one element for each row of the counts matrix), which can be read with the accessor function `conditions`.

In the following analysis steps, further data slots are populated. First, the size factors can be estimated with `estimateSizeFactors`, which are afterwards accessible via `sizeFactors`. Then, the dispersions (variance fits) are estimated with `estimateDispersions`. The resulting estimates are stored in phenoData columns, accessible via `pData`, with the column names staring with `disp_`. The intermediate steps of the fit are stored in the environment-values slot `fitInfo` (see `estimateDispersions` for details).

Internally, the mentioned data is stored in slots as follows:

As `CountDataSet` is derived from `eSet`, it has a `phenoData` slot which allows to store sample annotation. This is used to store the factor with the conditions, as a data frame column named `condition`, and to store the size factors, as an numeric data frame column named `sizeFactor`. If the user creates an object with multivariate design, i.e., passes a data frame instead of a factor for `conditions`, this data frame's columns are placed in the `phenoData` slot instead of the `condition` column. Furthermore, the function `estimateDispersions` adds columns with the dispersion values to be used by `nbinomTest` and `fitNbinomGLMs`. These columns have names starting with `disp_`.

The user may add further columns to the `phenoData` AnnotatedDataFrame.

The counts table is stored in the `eSet`'s `assayData` locked environment with the name `counts`.

The slot `dispInfo` is an environment containing lists, one for each set of estimated dispersion values and the slot `dispTable` (with accessor `dispTable` shows the assignment of conditions to dispersion estimates. See `estimateDispersions`

### Examples

    # See the vignette

[Package DESeq version 1.38.0 Index]