Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments
Fig 2
Performance benchmark and validity of the results.
Benchmarking the running time of Metheor using (A) simulated RRBS dataset and (B) Ewing sarcoma RRBS dataset. Values below the name of each of the measures denote the amount of speedup (in fold) in Metheor compared to its benchmark counterpart. Benchmarking the memory usage of Metheor using (C) simulated RRBS dataset and (D) Ewing sarcoma RRBS dataset. Values below the name of each of the measures denote the amount of memory usage reduction (in fold) in Metheor compared to its benchmark counterpart. All the benchmark experiments were repeated for three times, except for MHL. Lines denote the average wall time and shades represent the 95% confidence interval. The wall time for MHL computation was measured for only once. (E) Validity of the results. CpG-wise (PDR, MHL, FDRP and qFDRP) and CpG quartet-wise (PM and ME) methylation heterogeneity levels were compared between Metheor and the corresponding reference implementations. Pearson’s correlation coefficient and corresponding p-values are shown for FDRP and qFDRP.