# 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

1 2 3 4 | ```
## S4 method for signature 'CD'
explo.plot(object, samples = NULL, ...)
## S4 method for signature 'CD'
dat2save(object)
``` |

### Arguments

`object` |
Object generated from |

`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 |

### 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