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Compute SuSiE-ASH TWAS weights

Source: R/fineMappingWrappers.R
susieAshWeights.Rd

Extracts coefficients from an existing SuSiE-ASH fit or fits `susieR::susie()` with `unmappable_effects = "ash"`.

Usage

susieAshWeights(
  X = NULL,
  y = NULL,
  susieAshFit = 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.

susieAshFit

Optional fitted SuSiE-ASH 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.

Value

Numeric vector of variant weights.

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.
susieAshWeights(susieAshFit = fit)
#>  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0