present_prediction_wp: Present Liblinear prediction results

Description Usage Arguments Examples

View source: R/predict_whole_proteom.R

Description

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

Usage

1
2
3
present_prediction_wp(positive_index_file_names, candi_index_file_names,
  prediction_score_file_names, test_label_file_names, candidate_df_Rds,
  specificity_level = 0.99, output_label)

Arguments

positive_index_file_names

An Rds file containing the names of indices for positive windows.

candi_index_file_names

An Rds file containing the names of indices for candidate(negative) windows.

prediction_score_file_names

An Rds file containing the file names of Liblinear predicted scores.

test_label_file_names

An Rds file containing the file names of the label of the test data.

candidate_df_Rds

An Rds file containing the data frame of all candiate sites information(generated by g_feature_wp)/

specificity_level

A numerical number indicating the specificity user requires the classifier to achieve, default set to 0.99

output_label

The string to tag the output files.

Examples

1
2
3
4
5
6
7
present_prediction_wp(positive_index_file_names = "ps_0103_pos_index_names.Rds",
                                 candi_index_file_names = "ps_0103_candi_index_names.Rds",
                                 prediction_score_file_names = "ps_0103_prediction_file_names.Rds",
                                 test_label_file_names = "ps_0103_test_label_names.Rds",
                                 candidate_df_Rds = "ps_0103_candidate.Rds",
                                 specificity_level = 0.99,
                                 output_label = "ps_0103")

ginnyintifa/PTMscape documentation built on Nov. 9, 2021, 10:39 p.m.