As far as I know in the methylation data they use ratio of methylated vs unmethylated reads. How do they overcome the problem of small number of reads? Let say for one specific position there are 4 methylated and 8 unmethylated reads. The ratio would be 4/8=1/2. On another position there are 40 methylated and 80 unmethalyted reads, ratio is again 1/2. However, one would trust the second position much more because the first could be an affect of an error etc.
So, how do they account for the low and high number of reads when calculating the ratios?