Description Usage Arguments Value References Examples
This function also calculates the frequencies of all k-mers in the sequence but alows maximum m mismatch. m<k.
1 | Mismatch_DNA(seqs, k = 3, m = 2, label = c())
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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. |
k |
This parameter can be a number which shows kmer. |
m |
This parametr shows muximum number of mismatches. |
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). |
This function returns a feature matrix. The number of rows is equal to the number of sequences and the number of columns depends on the rng vector. For each value k in the vector, (4)^k columns are created in the matrix.
Liu, B., Gao, X. and Zhang, H. BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches. Nucleic Acids Res (2019).
1 2 | fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
mat<-Mismatch_DNA(seqs=fileLNC)
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