PseEIIP {ftrCOOL}

Pseudo Electron-Ion Interaction Pseudopotentials of Trinucleotide (PseEIIP)

Description

This function calculates the pseudo electron-ion interaction for each sequence. It creates a feature vector for each sequence. The vector contains a value for each for each tri-nucleotide. The value is computed by multiplying the aggregate value of electron-ion interaction of each nucleotide

Usage

PseEIIP(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

This function returns a feature matrix which the number of rows is equal to the number of sequences and the number of columns is 4^3=64.

References

Chen, Zhen, et al. "iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data." Briefings in bioinformatics 21.3 (2020): 1047-1057.

Examples

LNCSeqsADR<-system.file("extdata/",package="ftrCOOL")
LNC50Nuc<-as.vector(read.csv(paste0(LNCSeqsADR,"/LNC50Nuc.csv"))[,2])
mat<-PseEIIP(seqs = LNC50Nuc)