present_prediction_t: Present Liblinear prediction results
In ginnyintifa/PTMscape:

Combine Liblinear prediction results and window, position informations of sites. Calculate score threshold at user specified sensitivity level.

present_prediction_t(flag_for_score_threshold_chosen = "reference",
  score_threshold, ptm_site, flanking_size = 12, SPIDER = T,
  pred_candidate_df_Rds_name, pred_score_file_name, positive_info_file,
  known_protein_fasta_file, n_fold = 2, lower_bound = -1, upper_bound = 1,
  liblinear_dir, feature_file_path, cvlog_path_name, specificity_level,
  output_label)

`flag_for_score_threshold_chosen`	A string indicating whether use reference score threshold or get from the user supplied training data, defalt set to "reference".
`score_threshold`	A numerical value between 0 to 1 indicating the reference score threshold (supply when in "reference")
`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.
`pred_candidate_df_Rds_name`	An Rds file containing the candidate data frame of the proteins to be predicted.
`pred_score_file_name`	A text file containing the predicted score for the proteins of interest.
`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.
`n_fold`	Number of folds used for training and prediction, 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`	Absolute path of Liblinear tool.
`feature_file_path`	Absolute path of the feature files.
`cvlog_path_name`	The path and name of the log files, which hold the details of Liblinear procedures.
`specificity_level`	A numerical number indicating the specificity user requires the classifier to achieve, default set to 0.99. Used only not in "reference" mode.
`output_label`	The string to tag the output files in threshold getting purpose.

present_prediction_t(flag_for_score_threshold_chosen = "cv",
                           score_threshold = NULL,
                           ptm_site = "S", flanking_size = 12,
                           pred_candidate_df_Rds_name = "ps_predict_candidate.Rds",
                           pred_score_file_name = "ps_predict_predict.tsv",
                           positive_info_file = "known_ps.tsv", 
                           known_protein_fasta_file = "known_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/",
                           output_path = "/data/ginny/test_package/",
                           cvlog_path_name = "/data/ginny/test_package/cvlog.txt",
                           specificity_level = 0.99,
                           output_label = "ps_target")