Description Usage Arguments Details Examples
Predict on targeted proteome.
1 2 3 4 5 6 | predict_on_targeted_proteome(ptm_site, flanking_size = 12, SPIDER = T,
positive_info_file, known_protein_fasta_file, predict_protein_fasta_file,
output_label_training, output_label_predict, lower_bound = -1,
upper_bound = 1, liblinear_dir, feature_file_path, cvlog_path_name,
specificity_level, n_fold = 2,
flag_for_score_threshold_chosen = "reference", score_threshold)
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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. |
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. |
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). |
n_fold |
The number of folds used for training and prediction in cross validation stage (default set to 2). |
flag_for_score_threshold_chosen |
A string indicating whether use reference score threshold or get from the user supplied training data (default set to "reference"). |
score_threshold |
A numerical value between 0 to 1 indicating the reference score threshold (required in "reference" mode). |
This function outputs the features generated from input files.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | predict_on_targeted_proteome = function (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",
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,
n_fold = 2,
flag_for_score_threshold_chosen = "cv",
score_threshold = NULL)
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