BASiNETEntropy

• Murilo Breve
• Matheus Pimenta
• Fabrício Lopes

Introduction

Instalation

install.packages("igraph")  
install.packages("randomForest")  
if (!requireNamespace("BiocManager", quietly = TRUE))  
    install.packages("BiocManager")  

BiocManager::install("Biostrings")  

Classification

mRNA - Directory of an FASTA file containing mRNA sequences.
lncRNA - Directory of an FASTA file containing lncRNA sequences.
sncRNA - Directory of an FASTA file containing lncRNA sequences, this parameter is optional.
trainingResult - The result of the training, (three or two matrices)
save_dataframe - Boolean. This parameter saves a .csv file with the features in the current directory. No file is created by default.
save_model - Boolean. This parameter saves a .rds file with the model in the current directory. No file is created by default.

Defining parameters:

mRNA <- system.file("extdata", "mRNA.fasta", package = "BASiNETEntropy")
lncRNA <- system.file("extdata", "ncRNA.fasta", package = "BASiNETEntropy")
library(BASiNETEntropy)
result <- classify(mRNA=mRNA, lncRNA=lncRNA)

To obtain the entropy sum curve:

n_mRNA <- 4; n_lncRNA <- 5; n_treshold <- 2
entropymeasures<-trainingresult[[4]][4]
entropythreshold<-trainingresult[[4]][2]
BASiNETEntropy::curveofentropy(entropymeasures,entropythreshold)

The entropy sum curve refers to the mRNA class, the threshold at point 986 is found. Therefore, the edges referring to points 1 to 986 will be selected, and the rest will be discarded.

Example of generated entropy curves:

Citation

If you use this software in your work, please cite our paper. (soon)