With the advent of high-throughput sequencing technology, bisulfite-sequencing-based DNA methylation profiling methods have emerged as the most promising approaches due to their single-base resolution and genome-wide coverage. However, statistical analysis methods for analyzing this type of methylation data are not well developed. Although the most widely used proportion-based estimation method is simple and intuitive, it is not statistically adequate in dealing with the various sources of noise in bisulfite-sequencing data. Furthermore, it is not biologically satisfactory in applications that require binary methylation status calls.