INSPEcT_model-class

show,INSPEcT_model-method

object


INSPEcT_model is a class able to store all the results of the modeling of synthesis, processing and degradation rates made via the method <code><a rd-options="" href="/link/modelRates?package=INSPEcT&version=1.2.2" data-mini-rdoc="INSPEcT::modelRates">modelRates</a></code> (slot ratesSpecs).
It also stores the criteria (slot parameter) to choose between the many models tested for each gene the one that better describes the data and the results. 
The slot simple is a flag that distinguish wheter the model contains the information of the introns or not.
In case not, the flag simple is set to TRUE. 
Also the method <code><a rd-options="" href="/link/makeSimModel?package=INSPEcT&version=1.2.2" data-mini-rdoc="INSPEcT::makeSimModel">makeSimModel</a></code> of class <code><a rd-options="" href="/link/INSPEcT-class?package=INSPEcT&version=1.2.2" data-mini-rdoc="INSPEcT::INSPEcT-class">INSPEcT-class</a></code> creates an object of class INSPEcT_model. 
This object will be used by <code><a rd-options="" href="/link/makeSimDataset?package=INSPEcT&version=1.2.2" data-mini-rdoc="INSPEcT::makeSimDataset">makeSimDataset</a></code> to generate a complete simulated data-set, whose classification performance can be tested.


INSPEcT (INference of Synthesis, Processing and
dEgradation rates in Time-Course experiments) analyses 4sU-seq
and RNA-seq time-course data in order to evaluate synthesis,
processing and degradation rates and asses via modeling the
rates that determines changes in mature mRNA levels.

Stefano de Pretis

INSPEcT

Analysis of 4sU-seq and RNA-seq time-course data

INSPEcT_model-class function

 <dl>
<dt><code>params</code></dt><dd>A list that defines thresholds and how to perform log likelihood ratio tests</dd> <dt><code>ratesSpecs</code></dt><dd>A list containing the modeling output</dd> <dt><code>simple</code></dt><dd>A logical that indicates whether the mode of INSPEcT is simple (no pre-mRNA and degradation rates) or not.</dd> </dl>

Slots

INSPEcT_model is a class able to store all the results of the modeling of synthesis, processing and degradation rates made via the method <code><a href="modelRates" rd-options="">modelRates</a></code> (slot ratesSpecs).
It also stores the criteria (slot parameter) to choose between the many models tested for each gene the one that better describes the data and the results. 
The slot simple is a flag that distinguish wheter the model contains the information of the introns or not.
In case not, the flag simple is set to TRUE. 
Also the method <code><a href="makeSimModel" rd-options="">makeSimModel</a></code> of class <code><a href="INSPEcT-class" rd-options="">INSPEcT-class</a></code> creates an object of class INSPEcT_model. 
This object will be used by <code><a href="makeSimDataset" rd-options="">makeSimDataset</a></code> to generate a complete simulated data-set, whose classification performance can be tested.

INSPEcT_model-class: An S4 class to represent models generated by INSPEcT

Description

Usage

Arguments

Value

Slots

Details