This function replaces each nucleotide in the input sequence with its electron-ion interaction value.
The resulting sequence is represented by a feature vector whose length is equal to the length of the sequence.
Please check the references for more information.
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.
outFormat
(output format) can take two values: 'mat'(matrix) and 'txt'. The default value is 'mat'.
outputFileDist
shows the path and name of the 'txt' output file.
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
The output depends on the outFormat parameter which can be either 'mat' or 'txt'. If outFormat is 'mat', the function returns a feature
matrix for sequences with the same length such that the number of columns is equal to the length of the sequences
and the number of rows is equal to the number of sequences. It is usable for machine learning purposes.
If the outFormat is 'txt', the output is written to a tab-delimited file.
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.
# NOT RUN {LNCSeqsADR<-system.file("extdata/",package="ftrCOOL")
LNC50Nuc<-as.vector(read.csv(paste0(LNCSeqsADR,"/LNC50Nuc.csv"))[,2])
mat<-EIIP(seqs = LNC50Nuc,outFormat="mat")
# }