Extracts coefficients from an existing SuSiE-ASH fit or fits `susieR::susie()` with `unmappable_effects = "ash"`.
Arguments
- X
Genotype matrix. Required when `susieAshFit` is NULL.
- y
Phenotype vector. Required when `susieAshFit` is NULL.
- susieAshFit
Optional fitted SuSiE-ASH object.
- retainFit
If TRUE, stores the fitted object as an attribute on the returned weights.
- ...
Additional arguments passed to `susieR::susie()` when fitting.
Examples
data(eqtlRegionExample)
X <- eqtlRegionExample$X[, 1:30]
y <- eqtlRegionExample$yRes
susieAshWeights(X, y)
#> HINT: nrow(X) = 415 >= 2 * ncol(X) = 60. Consider precomputing sufficient statistics with compute_suff_stat() and fitting with susie_ss() instead -- this avoids holding X in memory at every iteration and lets you reuse XtX across multiple y.
#> HINT: For SuSiE-ash, slot_prior was not specified; using default Beta(a=1, b=2), roughly expecting ~3 of 10 slots to be active. Set slot_prior = slot_prior_betabinom(a, b) to override; for an uninformative prior use slot_prior_betabinom(1, 1).
#> chr22:32119788:T:C chr22:32119867:T:G chr22:32119961:T:G chr22:32120053:T:C
#> -4.948975e-04 -4.959149e-04 1.260941e-04 -7.967104e-05
#> chr22:32120593:A:G chr22:32120636:T:C chr22:32120932:G:A chr22:32120975:A:G
#> -7.969909e-05 -2.211048e-04 -3.163462e-04 4.383009e-04
#> chr22:32121290:C:T chr22:32121498:A:C chr22:32121635:T:G chr22:32121702:A:G
#> -6.600298e-05 -6.608065e-05 -1.207769e-04 -2.867932e-04
#> chr22:32121936:G:A chr22:32122351:A:G chr22:32122676:A:G chr22:32123055:A:G
#> -8.104677e-05 -5.526831e-05 -1.208567e-04 4.384386e-04
#> chr22:32123164:T:C chr22:32123383:T:C chr22:32123461:T:C chr22:32123806:C:T
#> -9.938075e-05 -9.841910e-05 4.029269e-04 -9.856865e-05
#> chr22:32124049:G:A chr22:32124126:C:T chr22:32124147:A:C chr22:32124381:G:A
#> -9.871971e-05 -2.217275e-04 -9.891881e-05 2.725441e-05
#> chr22:32124644:A:G chr22:32124683:T:C chr22:32124952:C:A chr22:32125308:A:G
#> -8.188025e-05 -2.220582e-04 -8.991323e-04 -3.720680e-04
#> chr22:32125638:A:C chr22:32125730:G:A
#> 2.285538e-04 3.011050e-04