Closed trb8 closed 3 years ago
I agree this would be useful, and is certainly something we have used ourselves in the past. If it is not yet an option we should add it.
On Fri, Aug 28, 2020 at 1:01 PM trb8 notifications@github.com wrote:
Hi Thanks for the great method/package. Will it be possible to report the per-SNP BFs (for each single effect) using e.g. s$snplbf[l,] <- res$lbf in update_each_effect_ss
Those BF will be useful for coloc analyses as in COLOC here https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1004383.s015&type=supplementary . The COLOC method itself assumes a single effect so there is a need.
Thanks, Tushar
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Great! Thank you.
Hi @trb8. I just want to make sure I understand your request.
The idea would be to create an output, let's call it lbf
, that is a p x L matrix, where p is the number of variables and L is the number of single effects, in which lbf[i,j]
is the log-Bayes factor for variable i and single effect j. Is that what you looking for?
@pcarbo sorry I have added it earlier but not tests and documentations to it yet ... I'll handle this and other issues #111 this evening on my calendar.
@pcarbo yes, that's what I meant Thanks @gaow
@trb8 susie
and susie_rss
now include an output lbf_variable
. It is a matrix containing the per-SNP Bayes factors. Please let us know if you have any questions about this, or anything else.
@trb8 I neglected to mention that this is implemented in the cran
branch.
Hi Thanks for the great method/package. Will it be possible to report the per-SNP BFs (for each single effect) using e.g. s$snplbf[l,] <- res$lbf in update_each_effect_ss
Those BF will be useful for coloc analyses as in COLOC here . The COLOC method itself assumes a single effect so there is a need.
Thanks, Tushar