Extracts coefficients from an existing SuSiE fit. from `X` and `y` before extracting weights.
Usage
susieWeights(
X = NULL,
y = NULL,
susieFit = NULL,
fitRetention = c("none", "slim", "full")
)Arguments
- X
Optional genotype matrix; when supplied it is only used to check that the fit covers the same number of variants.
- y
Unused; retained for signature compatibility.
- susieFit
Optional fitted SuSiE object.
- fitRetention
How much of the fit is kept on the returned weights:
"none"attaches nothing,"slim"and"full"attach it as the"fit"attribute. These extractors hold no trimmable intermediates, so the two retaining levels behave alike here.
Examples
data(eqtlRegionExample)
X <- eqtlRegionExample$X[, 1:30]
y <- eqtlRegionExample$yRes
fit <- susieR::susie(X, y, L = 5)
#> 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.
susieWeights(susieFit = fit)
#> chr22:32119788:T:C chr22:32119867:T:G chr22:32119961:T:G chr22:32120053:T:C
#> 0 0 0 0
#> chr22:32120593:A:G chr22:32120636:T:C chr22:32120932:G:A chr22:32120975:A:G
#> 0 0 0 0
#> chr22:32121290:C:T chr22:32121498:A:C chr22:32121635:T:G chr22:32121702:A:G
#> 0 0 0 0
#> chr22:32121936:G:A chr22:32122351:A:G chr22:32122676:A:G chr22:32123055:A:G
#> 0 0 0 0
#> chr22:32123164:T:C chr22:32123383:T:C chr22:32123461:T:C chr22:32123806:C:T
#> 0 0 0 0
#> chr22:32124049:G:A chr22:32124126:C:T chr22:32124147:A:C chr22:32124381:G:A
#> 0 0 0 0
#> chr22:32124644:A:G chr22:32124683:T:C chr22:32124952:C:A chr22:32125308:A:G
#> 0 0 0 0
#> chr22:32125638:A:C chr22:32125730:G:A
#> 0 0