predict_with_liblinear: Process prediction with Liblinear

Description Usage Arguments Details Examples

View source: R/predict_targetted.R

Description

Process the feature files with Liblinear training and prediction. Train on known proteins and predict on unknown proteins

Usage

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predict_with_liblinear(liblinear_dir, feature_file_path, training_file_name,
  test_file_name, output_label, cvlog_path_name)

Arguments

liblinear_dir

Absolute path of Liblinear tool.

feature_file_path

Absolute path of the feature files.

training_file_name

A string indicating file name of the training feature data.

test_file_name

A string indicating the file name of the test feature data.

output_label

The string to tag the output files.

cvlog_path_name

The path and name of the log files, which hold the details of Liblinear procedures.

Details

This function call Liblinear library to perform n_fold training/prediction, the prediction score will be part of the output files.

Examples

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predict_with_liblinear(liblinear_dir = "/data/ginny/liblinear-2.11/",
                      feature_file_path = "/data/ginny/test_package/",
                      training_file_name = "ps_predict_train_feature_svm.tsv",
                      test_file_name = "ps_predict_test_feature_svm.tsv",
                      output_label = "ps_predict",
                      cvlog_path_name = "/data/ginny/test_package/cvlog.txt")

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