Effect size estimates

[joshchiou]

Is there a way to recover (or approximate) the per-variant effect size estimates for each signal/credible set? From my limited understanding, mu contains the posterior z-scores for each signal. Is there a simple solution that I'm missing here? (e.g. mu * sqrt(posterior variance))?

Thanks, Josh

[stephens999]

Are you using susie or susie_rss?

On Wed, Jun 2, 2021, 00:29 Josh Chiou @.***> wrote:

Is there a way to recover (or approximate) the per-variant effect size estimates for each signal/credible set? From my limited understanding, mu contains the posterior z-scores for each signal. Is there a simple solution that I'm missing here? (e.g. mu * sqrt(posterior variance))?

Thanks, Josh

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[joshchiou]

I'm using susie_rss.

[stephens999]

To get effect estimates use 'susie_get_posterior_mean'

If you used susie_rss you need to multiply those estimates by the original standard errors (ie by s_j if z_j= bhat_j/s_j) to get estimates on the original scale.

Note that these are unconditional effect estimates (ie scaled by the pips). Thus if a snp is in ld with a lot of other snps it's unconditional effect estimate will tend to be small because its pip will tend to be small.

On Wed, Jun 2, 2021, 18:24 Josh Chiou @.***> wrote:

I'm using susie_rss.

Are you using susie or susierss? … <#m-3668851743586760740_m_8177645735469955484_m8895739208112277259> On Wed, Jun 2, 2021, 00:29 Josh Chiou @.**> wrote: Is there a way to recover (or approximate) the per-variant effect size estimates for each signal/credible set? From my limited understanding, mu contains the posterior z-scores for each signal. Is there a simple solution that I'm missing here? (e.g. mu sqrt(posterior variance))? Thanks, Josh — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#129 https://github.com/stephenslab/susieR/issues/129>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANXRRNH5YCFZG5WP6ZFPU3TQW6TNANCNFSM456AOISQ .

I'm using susie_rss.

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