modelInfo-class

modelInfo

$,modelInfo-method

$<-,modelInfo-method


  An object of class <code>"modelInfo"</code> represents the information of sequence to use in the analysis


classes

This package uses the Naive Bayes classifier (from e1071)
to assign probability values to putative polyadenylation sites
(pA sites) based on training data from zebrafish. This will
allow the user to separate true, biologically relevant pA sites
from false, oligodT primed pA sites.

Sarah Sheppard

cleanUpdTSeq

This package classifies putative polyadenylation sites as true
or false/internally oligodT primed

modelInfo-class function

Objects can be created by calls of the form <code>new("modelInfo", upstream, downstream, wordSize, alphabe, genome)</code>.

Objects from the Class

<dl>
    <dt>genome</dt><dd>
Name of the genome to use to get sequence. To find out a list of available genomes, please type available.genomes() in R.
</dd> <dt>upstream</dt><dd>
This is the length of upstream sequence to use in the analysis.
</dd> <dt>downstream</dt><dd>
This is the length of downstream sequence to use in the analysis.
</dd> <dt>wordSize</dt><dd>
This is the size of the word to use as a feature for the upstream sequence. wordSize = 6 should always be used. </dd> <dt>alphabet</dt><dd>
These are the bases to use, for example DNA bases ACTG.
</dd> </dl> 

Slots

<dl>
        <dt>$, $&lt;-</dt><dd>Get or set the slot of <code><a rd-options="" href="/link/modelInfo?package=cleanUpdTSeq&version=1.10.2" data-mini-rdoc="cleanUpdTSeq::modelInfo">modelInfo</a></code></dd> </dl> 

Methods

An object of class <code>"modelInfo"</code> represents the information of sequence to use in the analysis

modelInfo-class: Class `"modelInfo"`

Description

Arguments

Objects from the Class

Slots

Methods