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Table 1 Performance assessment for IMR-90 analysis (chromosome 7)

From: BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach

SssI depth Number of bins Method Mean bias Mean of squared differences Spearman correlation Wald Highest posterior density Quantile
[ 0,4] 305,638 BayMeth -0.04 0.08 0.36 0.74 0.89 0.89
   BayMeth (SssI-free) -0.19 0.20 0.23 0.24
   Batman 0.22 0.14 0.31 0.43
   MEDIPS -0.38 0.26 0.29
   BALM -0.48 0.33 0.32
(4,7] 22,196 BayMeth 0.05 0.05 0.65 0.84 0.88 0.87
   BayMeth (SssI-free) -0.01 0.08 0.42 0.68
   Batman 0.16 0.07 0.61 0.34
   MEDIPS -0.23 0.11 0.45
   BALM -0.27 0.15 0.60
(7,14] 28,871 BayMeth 0.06 0.04 0.69 0.84 0.86 0.86
   BayMeth (SssI-free) 0.02 0.05 0.57 0.79
   Batman 0.16 0.07 0.65 0.28
   MEDIPS -0.21 0.10 0.49
   BALM -0.21 0.11 0.66
(14,27] 28,928 BayMeth 0.05 0.03 0.76 0.81 0.85 0.82
   BayMeth (SssI-free) 0.08 0.04 0.72 0.70
   Batman 0.15 0.06 0.73 0.23
   MEDIPS -0.20 0.09 0.59
   BALM -0.15 0.07 0.75
(27,168] 28,719 BayMeth 0.02 0.03 0.79 0.73 0.86 0.78
   BayMeth (SssI-free) 0.11 0.04 0.77 0.48
   Batman 0.11 0.05 0.75 0.20
   MEDIPS -0.22 0.10 0.67
   BALM -0.14 0.06 0.76
  1. Results are shown for bins with a truth depth larger than the 25% quantile (cutoff is 33 reads), stratified into five groups by SssI depth. Shown are the number of bins per group, mean bias, MSE, Spearman correlation and coverage probabilities at 95% level.