GCcontentBias: GCbias class

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

Description

GCbias class generated from dat() function with type="GCbias". This object contains the trimmed mean of expression for each GC content bin of 200 features per sample or condition and also per biotype (if available). It also includes the corresponding spline regression model fitted to explain the relationship between length and expression.

Usage

## S4 method for signature 'GCbias'
explo.plot(object, samples = NULL, toplot = "global", ...)
## S4 method for signature 'GCbias'
dat2save(object)

Arguments

object	Object generated with dat() function.
toplot	Biological group to be plotted (features not belonging to that group are discarded). It may be a number or a text with the name of the biological group. If toplot=1 or toplot="global", all features are used for the plot.
samples	Samples (or conditions) to be plotted. If NULL, all the samples are plotted. If samples > 2, only a descriptive plot will be generated. If not, diagnostic plots will be obtained showing both the R-squared and model p-value from the spline regression model describing the relationship between the GC content and the expression.
...	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:

data2plot: A list with as many elements as biological groups (the first element correspond to all the features). Each element of the list is a matrix containing the GC content bins in the first column and an additional column for the trimmed mean expression per bin for each sample or condition. RegressionModels: A list with as many elements as samples or conditions. Each element is an "lm" class object containing the spline regression model relating GC content and expression for that sample or condition (considering all the features).

Methods

This class has an specific show method to print a summary of spline regression models and a dat2save method to save the GC content bin information. 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.