CD: CD class

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

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

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