CD {NOISeq} | R Documentation

## CD class

### Description

CD class generated from dat() function with type="cd". This object contains the distributions of log-fold changes (M values) between each of the samples and a reference sample as well as confidence intervals for the median of these distributions that are used to detect a potential RNA composition bias in the data.

### Usage

    ## S4 method for signature 'CD'
    explo.plot(object, samples = NULL, ...)
    ## S4 method for signature 'CD'
    dat2save(object)

### Arguments

`object` | Object generated from `dat()` function.
`samples` | Samples or conditions to be plotted. If NULL, the twelve first samples are plotted because the plot for this object only admit a maximum of twelve samples.
`...` | Any argument from `par`.

### Slots/List Components

Objects of this class contain (at least) the following list components:

`dat`: List containing the following elements:

`data2plot`: Data frame where each column contains the M values obtained as the log2-ratio of each sample against the reference sample. `refColumn`: Column number in input data that is taken as the reference sample. `DiagnosticTest`: Data frame that contains the lower and upper limits of the confidence intervals for the median of M values per each sample. The last column indicates if the diagnostic test for that sample has been passed or failed (so normalization has to be applied).

### Methods

This class has an specific `show` method in order to show the confidence intervals for the M median and a `dat2save` method to save the relevant information in the object in a user-friendly way. It also has an `explo.plot` method to plot the data contained in the object.

### Author(s)

Sonia Tarazona

[Package NOISeq version 2.38.0 Index]