Biodetection: Biodetection class

Description

Biodetection class generated from dat() function with type="biodetection". This object contains the percentage of each biological class (e.g. biotype) in the genome (i.e. in the whole set of features provided), the corresponding percentage detected by the sample and the percentage of the biotype within the sample.

Usage

"explo.plot"(object, samples = c(1, 2), plottype = c("persample", "comparison"), toplot = "protein_coding", ...)
"dat2save"(object)

Arguments

object

Object generated from dat() function.

samples

Samples or conditions to be plotted. If NULL, the two first samples are plotted because the plot for this object only admit a maximum of two samples.

plottype

If plottype="persample", each sample is plotted in a separate plot displaying abundance of byotype in genome, percentage of biotype detected by sample and abundance of biotype in sample. If plottype="comparison", two samples can be compared in the same plot. Two plots are generated, one for the percentage of biotype detected by each of the compared samples, and the other for the abundance of the biotypes within the compared samples.

toplot

If plottype="comparison" and a biotype is specified in this argument (by default toplot="protein_coding"), a proportion test is performed to test if the abundance of that biotype is significantly different for the two samples being compared.

...

Any argument from par.

Slots/List Components

An object of this class contains an element (dat) which is a list with the following components: genome: Vector containing the percentage of features per biotype in the genome. biotables: List with as many elements as samples or conditions. Each element of the list contains the percentage of features in the genome per biotype detected in that sample or condition features per biotype and the percentage of detected features in the sample or condition per biotype.

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.