ANF_RNA: Accumulated riboNucleotide Frequency (ANF_RNA)
In ftrCOOL: Feature Extraction from Biological Sequences

Description Usage Arguments Value Note References Examples

This function replaces ribonucleotides with a four-length vector. The first three elements represent the ribonucleotides and the forth holds the frequency of the ribonucleotide from the beginning of the sequence until the position of the ribonucleotide in the sequence. 'A' will be replaced with c(1, 1, 1, freq), 'C' with c(0, 1, 0, freq),'G' with c(1, 0, 0, freq), and 'U' with c(0, 0, 1, freq).

1	ANF_RNA(seqs, outFormat = "mat", outputFileDist = "", label = c())

`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.
`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).

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 (sequence length)*(4) and the number of rows is equal to the number of sequences. If the outFormat is 'txt', the output is written to a tab-delimited file.

This function is provided for sequences with the same lengths. Users can use 'txt' option in outFormat for sequences with different lengths. Warning: If outFormat is set to 'mat' for sequences with different lengths, it returns an error. Also, when output format is 'txt', label information is not shown in the text file. It is noteworthy that 'txt' format is not usable for machine learning purposes if sequences have different sizes. Otherwise 'txt' format is also usable for machine learning purposes.

Chen, W., Tran, H., Liang, Z. et al. Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome. Sci Rep 5, 13859 (2015).