Allele-specific methylation

-p_AS

The proportion of allele-specific methylations. For example,

-p_AS 0.2

Approximately 20% of methylation blocks will have allele-specific methylations.

-r_methylated_father

Ratio of the father-specific methylation rate. Methylation rate for the paternal allele at a CpG will be r_methylated_father*p, where p is the methylation rate for the CpG from the profile.
For example,

-r_methylated_father 1.2

Assume p is 0.8. Methylation rate for the paternal allele will be 0.96.

-r_methylated_mother

Ratio of the mother-specific methylation rate. Methylation rate for the maternal allele at a CpG will be r_methylated_mother*p, where p is the methylation rate for the CpG from the profile.