createGraph2D

For an analysis of each measure, the createGraph2D () function was created in order to visualize the behavior of each measurement in relation to the threshold. This function creates a graph (Measure x Threshold) from an array, mRNA sequences are given the blue color, the lncRNA sequences are given a red color. In cases where there is a third class this will be given the green color

It makes the creation of networks from sequences of RNA, with this is done the abstraction of characteristics of these networks with a methodology of threshold for the purpose of making a classification between the classes of the sequences. There are four data present in the 'BASiNET' package, "sequences", "sequences2", "sequences-predict" and "sequences2-predict" with 11, 10, 11 and 11 sequences respectively. These sequences were taken from the data set used in the article (LI, Aimin; ZHANG, Junying; ZHOU, Zhongyin, 2014) <doi:10.1186/1471-2105-15-311>, these sequences are used to run examples. The BASiNET was published on Nucleic Acids Research, (ITO, Eric; KATAHIRA, Isaque; VICENTE, Fábio; PEREIRA, Felipe; LOPES, Fabrício, 2018) <doi:10.1093/nar/gky462>.

Fabricio Martins Lopes

BASiNET

Classification of RNA Sequences using Complex Network Theory

Eric Augusto Ito

createGraph2D function

<dl><dt>matrix</dt>
<dd>matrix of the measure for the creation of two-dimensional graph</dd>
<dt>numSeqMRNA</dt>
<dd>Integer number of mRNA sequences</dd>
<dt>numSeqLNCRNA</dt>
<dd>Integer number of lncRNA sequences</dd>
<dt>nameMeasure</dt>
<dd>Character Parameter that defines the name of the measure to put in the title of the graph</dd></dl>

Arguments

Author

Creates a two-dimensional graph between a measure and the threshold — createGraph2D

<dl>

<dt>matrix</dt>
<dd>matrix of the measure for the creation of two-dimensional graph</dd>


<dt>numSeqMRNA</dt>
<dd>Integer number of mRNA sequences</dd>


<dt>numSeqLNCRNA</dt>
<dd>Integer number of lncRNA sequences</dd>


<dt>nameMeasure</dt>
<dd>Character Parameter that defines the name of the measure to put in the title of the graph</dd>

</dl>

createGraph2D: Creates a two-dimensional graph between a measure and the threshold

Description

Usage

Arguments

Author