Saturation: Saturation class

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

Description

Saturation class generated from dat() function with type="saturation". This object contains the number of detected features per biotype at increasing sequencing depths and also the new detections per each million of new sequencing reads.

Usage

## S4 method for signature 'Saturation'
explo.plot(object, samples = NULL, toplot = 1, yleftlim = NULL, yrightlim = NULL, ...)
## S4 method for signature 'Saturation'
dat2save(object)

Arguments

object	Object generated from dat() function.
toplot	This parameter indicates which biological group is to be plotted. It may be a number or a text with the name of the biological group. If toplot=1 (or "global"), a global plot considering features from all the biological groups will be generated.
samples	The samples to be plotted. If NULL, all the samples are plotted for Saturation object.
yleftlim	Range for Y left-axis (on the left-hand side of the plot) when new detections are plotted (this occurs when the number of samples to be plotted is 1 or 2). If NULL (default), an appropriate range is computed.
yrightlim	Range for Y right-axis (on the right-hand side of the plot) when new detections are plotted (this occurs when the number of samples to be plotted is 1 or 2). If NULL (default), an appropriate range is computed.
...	Any argument from par.

Slots/List Components

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

dat: List containing the information generated by dat() function. This list has the following elements:

saturation: List containing for all the biological classes (and also a global class with all of them together) the saturation data to be plotted for each sample (in Y left axis).

bionum: Vector containing for all the biological classes (and also a global class with all of them together) the number of features for that group.

depth: List containing for each selected sample the increasing values of sequencing depth to be plotted.

newdet: List containing for all the biological classes (and also a global class with all of them together) the new detection data to be plotted for each selected sample (in Y right axis).

real: List with as many elements as the number of biological classes (plus one for the global). Each element contains the real sequencing depth for each sample and the corresponding number of detected features at that sequencing depth.

Methods

This class has an specific show method in order to work and print a summary of the elements which are contained and a dat2save method to save the relevant information in an object cleanly. 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.