predict_on_whole_proteome: A function to predict and annotate whole proteom PTM sites
In ginnyintifa/PTMscape:

Description Usage Arguments Details Examples

A function to predict and annotate whole proteom PTM sites

predict_on_whole_proteome(ptm_site, flanking_size = 12, SPIDER = T,
  positive_info_file, protein_fasta_file, n_fold = 2, lower_bound = -1,
  upper_bound = 1, liblinear_dir, feature_file_path, cvlog_path_name,
  specificity_level = 0.99, output_label)

`ptm_site`	The target amino acid of the given PTM type, 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 whether to use SPIDER3 features (default set to TRUE.)
`positive_info_file`	A text file containing the positive PTM sites in the required format.
`protein_fasta_file`	A text file containing the protein sequences of interest in fasta format.
`n_fold`	The number of folds used for training and prediction in cross validation stage (default set to 2).
`lower_bound`	The lower bound of the scaled data range (default to -1).
`upper_bound`	The upper bound of the scaled data range (default to 1).
`liblinear_dir`	The path for the Liblinear tool.
`feature_file_path`	The path for the feature files.
`cvlog_path_name`	The path and name of the log files, which hold the details of Liblinear procedures.
`specificity_level`	A number ranges from 0 to 1 indicating the specificity user requires the classifier to achieve (default to 0.99).
`output_label`	The string to tag the output files.

This function outputs the features generated from input files.

predict_on_whole_proteome(ptm_site = "S",
                         flanking_size = 12,
                         SPIDER = T,
                         positive_info_file = "ps_PSP.tsv",
                         protein_fasta_file = "S_sp_fasta.tsv",
                         n_fold = 2,
                         lower_bound = -1,
                         upper_bound = 1,
                         liblinear_dir = "/data/ginny/liblinear-2.11/",
                         feature_file_path = "/data/ginny/test_package/",
                         cvlog_path_name = "/data/ginny/test_package/cvlog.txt",
                         specificity_level = 0.99,
                         output_label = "ps_0103")