README.txt

February 12, 2020 · View on GitHub

R scripts:

  1. calculate_sensitivity.R This is the last version of CSS calculation for drug combinations and sensitivity (relative inhibition - RI) calculation for single agents. Datasets, such as single_drug_data.RData and combo_drug_data.RData can be utilized to calculate those scores.

  2. predicion_of_css.Rmd The script predicts the CSS for drug combinations from css_data.RData using drug target information from fingerprints.RData, primary_targets.RData and primary_plus_sea_targets.RData, and machine learning methods (Elastic Net, Random Forests, Support Vector Machines). R2, RMSE, MAE and correlation values are calculated for a selected cell line and machine learning method.

RData files:

  1. single_drug_data.RData A file that can be used in calculate_sensitivity.R to calculate relative inhibition (RI) for single drug experiments. The file has to contain such columns as cellLine, drug, dose and viability.

  2. combo_drug_data.RData A file that can be used in calculate_sensitivity.R to calculate CSS for combination drug experiments. The file has to contain such columns as cellLine, drugA, drugAdose, drugB, drugBdose and viability.

  3. fingerprints.RData A file that can be used in predicion_of_css.Rmd to build a matrix of features. It contains binary fingerprint data mapped to the drugs used in the experiment. It has to contain column with drug names named ‘drug’.

  4. primary_targets.RData A file that can be used in predicion_of_css.Rmd to build a matrix of features. It contains binary primary drug target data mapped to the drugs used in the experiment. It has to contain column with drug names named ‘drug’.

  5. primary_plus_sea_targets.RData A file that can be used in predicion_of_css.Rmd to build a matrix of features. It contains binary primary drug target data and drug targets that were identified using SEA method mapped to the drugs used in the experiment. It has to contain column with drug names named ‘drug’.

  6. css_data.RData A file that can be used in predicion_of_css.Rmd. The file provides CSS data that were calculated using calculation_of_css.Rmd. It has to contain columns with both drug names named ‘drug1’ and ‘drug2’, cell lines specified in column ’cellLine’ and CSS column names ‘CSS’.