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LD score calculation #9

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xiangzhu opened this issue Jul 31, 2018 · 1 comment
Open

LD score calculation #9

xiangzhu opened this issue Jul 31, 2018 · 1 comment
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@xiangzhu
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xiangzhu commented Jul 31, 2018 •
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It seems that the current LD score calculation is different from the authors' approach.

https://github.com/stephenslab/LDshrink/blob/32b4ad3942f7cb429f23c529b86ab72cfbb1b257/R/block_utils.R#L117

Below is the 2nd paragraph of the first LDSC paper online method: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495769/

screen shot 2018-07-31 at 12 35 18 pm
@xiangzhu
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xiangzhu commented Aug 7, 2018

Note that \hat{r}^2_{adj} above is also a "shrinkage" estimator of LD: it's value is always no greater than the corresponding \hat{r}^2. Hence, it also fits well into LDshrink (and we probably should implement it).

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