| MMI_DNA {ftrCOOL} | R Documentation |
Multivariate Mutual Information_DNA (MMI_DNA)
Description
MMI computes mutual information based on 2-mers T2 = AA, AC, AG, AT, CC, CG, CT, GG, GT, TT and 3-mers T3 = AAA, AAC, AAG, AAT, ACC, ACG, ACT, AGG, AGT, ATT, CCC, CCG, CCT, CGG, CGT, CTT, GGG, GGT, GTT and TTT for more information please check the reference part.
Usage
MMI_DNA(seqs, label = c())
Arguments
seqs |
is a FASTA file containing nucleotide sequences. The sequences start with '>'. Also, seqs could be a string vector. Each element of the vector is a nucleotide 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 nucleic acid and protein sequence analysis, prediction and visualization, Nucleic Acids Research (2021).
Examples
fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
mat<-MMI_DNA(seqs=fileLNC)