How to define cpg site at overlapping cis windows?

[hsun3163]

As per our discussion, we will define the molecular phenotype object of cpg site by a cis window around the TSS of each gene. However, one of the problems of this approach is how to handle the cpg site that is presented at the intersection of two cis windows.

Previously in the TWAS project, we handle the similar problem with SNP by assigning them to different genes simultaneously and creating two SNP-gene pairs.

However, in the tensorQTL setting, the phenotype vs phenotype-group relationship is required to be unique. As indicates below, each ID can only be included into 1 phenotype group, and assigned with 1 TSS (and hence 1 cis window)

chr	start	end	ID	Group
1	1000	1001	A	G1
1	1000	1001	B	G1
1	2000	2001	C	G2
1	2000	2001	D	G2