knnAUC: an open-source R package for detecting nonlinear dependence between one continuous variable and one binary variable

• Main Authors: Yi Li, Xiaoyu Liu, Yanyun Ma, Yi Wang, Weichen Zhou, Meng Hao, Zhenghong Yuan, Jie Liu, Momiao Xiong, Yin Yao Shugart, Jiucun Wang, Li Jin
• Format: Article
• Language: English
• Published: BMC 2018-11-01
• Series: BMC Bioinformatics
• Subjects: Open source; R package; Nonlinear dependence; One continuous variable; One binary dependent variable; AUC
• Online Access: http://link.springer.com/article/10.1186/s12859-018-2427-4

Abstract Background Testing the dependence of two variables is one of the fundamental tasks in statistics. In this work, we developed an open-source R package (knnAUC) for detecting nonlinear dependence between one continuous variable X and one binary dependent variables Y (0 or 1). Results We addressed this problem by using knnAUC (k-nearest neighbors AUC test, the R package is available at https://sourceforge.net/projects/knnauc/). In the knnAUC software framework, we first resampled a dataset to get the training and testing dataset according to the sample ratio (from 0 to 1), and then constructed a k-nearest neighbors algorithm classifier to get the yhat estimator (the probability of y = 1) of testy (the true label of testing dataset). Finally, we calculated the AUC (area under the curve of receiver operating characteristic) estimator and tested whether the AUC estimator is greater than 0.5. To evaluate the advantages of knnAUC compared to seven other popular methods, we performed extensive simulations to explore the relationships between eight different methods and compared the false positive rates and statistical power using both simulated and real datasets (Chronic hepatitis B datasets and kidney cancer RNA-seq datasets). Conclusions We concluded that knnAUC is an efficient R package to test non-linear dependence between one continuous variable and one binary dependent variable especially in computational biology area.