isGPT: An optimized model to identify sub-Golgi protein types using SVM and random forest based feature selection
Necessary Software Tools to install before working with CRISPRpred:
- e1071, caTools, ROCR and randomForest R packages *You can install it by typing 'install.packages('e1071')' in your R console.
#isGPT works in following steps#
#Step 1: It extracts features using featurization.R, trainingset.csv and testingset.csv files.#
*Open the base.R file and set the file name in it.
Your file must be in the same directory as featurization.R file.
*Run base.R file and this will generate features accordingly
and save featurized training data in featurized_304_posTrimer.rds and featurized testing data in testFile_64_posTrimer.rds.
#Step 2: Then it runs a wrapper feature selection algorithms of randomForest R package using base.R#
*The model returned by randomForest will be saved in rfmodel_304_posTrimer.rds file.
#Step 3: In this step, an optimized model is build using createModel.R file.#
*The best model is saved in svm_304_posTrimer.rds file.
#Step 4: It performs different testing strategies.#
*Run testModel.R file for independent testing.
*Run alltestings.R for jackknife testing.
*Run createModel.R for 10-fold cross-validation which saved resutls in Step 3.
*All the above files generate results for classification model. All files with '*reg*' or '*regression*' extensions, generate results for regression model.
isGPT tool is developed by Md. Khaledur Rahman. If you need any help, please contact: khaled.cse.07@gmail.com
Credits: M. Saifur Rahman and M. Sohel Rahman