ftrCOOL (version 2.0.0)

MMI_RNA: Multivariate Mutual Information_RNA (MMI_RNA)

Description

MMI computes mutual information based on 2-mers T2 = AA, AC, AG, AU, CC, CG, CU, GG, GU, U and 3-mers T3 = AAA, AAC, AAG, AAU, ACC, ACG, ACU, AGG, AGU, AUU, CCC, CCG, CCU, CGG, CGU, CUU, GGG, GGU, GUU and UUU for more information please check the reference part.

Usage

MMI_RNA(seqs, label = c())

Arguments

seqs

is a FASTA file containing ribonucleotide sequences. The sequences start with '>'. Also, seqs could be a string vector. Each element of the vector is a ribonucleotide sequence.

label

is an optional parameter. It is a vector whose length is equivalent to the number of sequences. It shows the class of each entry (i.e., sequence).

Value

It is a feature matrix. The number of columns is 30 and the number of rows is equal to the number of sequences.

References

Zhen Chen, Pei Zhao, Chen Li, Fuyi Li, Dongxu Xiang, Yong-Zi Chen, Tatsuya Akutsu, Roger J Daly, Geoffrey I Webb, Quanzhi Zhao, Lukasz Kurgan, Jiangning Song. iLearnPlus: a comprehensive and automated machine-learning platform for ribonucleic acid and protein sequence analysis, prediction and visualization, Nucleic Acids Research (2021).

Examples

# NOT RUN {
fileLNC<-system.file("extdata/Carica_papaya101RNA.txt",package="ftrCOOL")
mat<-MMI_RNA(seqs=fileLNC)
# }