generate_feature_t: Generate feature data for targeted proteome.
In ginnyintifa/PTMscape:

Description Usage Arguments Details Examples

This function generates feature data for targeted by mapping the positive PTM info to protein sequences, constructing windows and extracting 3 sets of features.

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generate_feature_t(ptm_site, flanking_size = 12, SPIDER = T,
  positive_info_file, known_protein_fasta_file, predict_protein_fasta_file,
  output_label_training, output_label_predict)

`ptm_site`	The amino acid this PTM involves, in upper-case single letter representation.
`flanking_size`	The number of residues surrounding each side of the center residue, the total window size will be 2*flanking_size+1, default to 12.
`SPIDER`	A boolean variable indicating the usage of SPIDER3 features, default set to TRUE.
`positive_info_file`	A text file containing the positive PTM sites info in required format.
`known_protein_fasta_file`	A text file containing the proteins sequences of interest and known PTM sites in Fasta format.
`predict_protein_fasta_file`	A text file containing the proteins sequences with PTM sites to be predicted in Fasta format.
`output_label_training`	The string to tag the output files associated with training proteins.
`output_label_predict`	The string to tag the output files associated with prediction proteins.

This function outputs the features generated from input files.

generate_feature_t(ptm_site = "S",
            flanking_size = 12,
            SPIDER = T,
            positive_info_file = "known_ps.tsv",
            known_protein_fasta_file = "known_fasta.tsv",
            predict_protein_fasta_file = "predict_fasta.tsv",
            output_label_training = "ps_training",
            output_label_predict = "ps_predict")