I had a couple of questions on PDM haplotypes identified using CPEL.
Q1 - The CPEL paper refers to PDM haplotypes that are significant p < 0.05 as genetically informative haplotypes and that the variant carries information on the methylation state of the allele/haplotype. Does this mean that the variant used to infer if the haplotype is significantly ASM lies on the same site as the methylated cytosine ?? Meaning the CpG site itself is a variant example C>T >> Or does it mean that the reads supporting the variant call overlap the CpG site - But this is the case for all haplotypes used by CPEL , thats my understanding, so it should be the former. Can you confirm how exactly is a PDM haplotype (p<0.05) genetically more informative than an MML or NME hap ??
Q2 - When we see a PDM value for a haplotype as 0.2 for example, does it mean that the haplotype has a 20% probability of being ASM ??
You insight would be very helpful inferring and understanding the biological value of the data from the terms above.
Hi Jordi,
I had a couple of questions on PDM haplotypes identified using CPEL.
Q1 - The CPEL paper refers to PDM haplotypes that are significant p < 0.05 as genetically informative haplotypes and that the variant carries information on the methylation state of the allele/haplotype. Does this mean that the variant used to infer if the haplotype is significantly ASM lies on the same site as the methylated cytosine ?? Meaning the CpG site itself is a variant example C>T >> Or does it mean that the reads supporting the variant call overlap the CpG site - But this is the case for all haplotypes used by CPEL , thats my understanding, so it should be the former. Can you confirm how exactly is a PDM haplotype (p<0.05) genetically more informative than an MML or NME hap ??
Q2 - When we see a PDM value for a haplotype as 0.2 for example, does it mean that the haplotype has a 20% probability of being ASM ??
You insight would be very helpful inferring and understanding the biological value of the data from the terms above.
Thank you Numrah