Compute SuSiE TWAS weights

Extracts coefficients from an existing SuSiE fit or fits `susieR::susie()` from `X` and `y` before extracting weights.

Usage

susieWeights(X = NULL, y = NULL, susieFit = NULL, retainFit = FALSE, ...)

Arguments

X

Genotype matrix. Required when `susieFit` is NULL.

y

Phenotype vector. Required when `susieFit` is NULL.

susieFit

Optional fitted SuSiE object.

retainFit

If TRUE, stores the fitted object as an attribute on the returned weights.

...

Additional arguments passed to `susieR::susie()` when fitting.

Value

Numeric vector of variant weights.

Examples

data(eqtlRegionExample)
X <- eqtlRegionExample$X[, 1:30]
y <- eqtlRegionExample$yRes
susieWeights(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.
#> 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