Could the "rg" part have the data of "intercept"? If it can be calculated, how do I make it?

[mglev1n]

Do you have a particular use-case in mind for the cross-trait intercept?

[MikeKiki101]

Do you have a particular use-case in mind for the cross-trait intercept?

I just want to use it for CC-GWAS analysis which needs cross trait intercept.

[mglev1n]

I think covariance_res$intercept which is created as part of the following line may represent the cross-trait intercept, but I'll need to do some comparisons with the original LDSC python package to double-check. https://github.com/mglev1n/ldscr/blob/7c8e1387bdd4f8f9dbc6f92a40e09d624b201b33/R/ldsc_rg.R#L262

Most of this package just implements the ldsc code from the GenomicSEM package (https://github.com/GenomicSEM/GenomicSEM) with a friendlier user-interface - I don't think they originally exposed the cross-trait intercept, which is why it will take a little investigation.

[MikeKiki101]

I think covariance_res$intercept which is created as part of the following line may represent the cross-trait intercept, but I'll need to do some comparisons with the original LDSC python package to double-check. https://github.com/mglev1n/ldscr/blob/7c8e1387bdd4f8f9dbc6f92a40e09d624b201b33/R/ldsc_rg.R#L262

Most of this package just implements the ldsc code from the GenomicSEM package (https://github.com/GenomicSEM/GenomicSEM) with a friendlier user-interface - I don't think they originally exposed the cross-trait intercept, which is why it will take a little investigation.

OK, thank you very much！I will figure it out！

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