Extract weights from mr.ash.rss (susieR)

Usage

mrashRssWeights(
  stat,
  ldReference,
  varY = NULL,
  sigma2E = NULL,
  s0 = NULL,
  w0 = NULL,
  fitRetention = c("none", "slim", "full"),
  methodArgs = MrashRssOptions()
)

Arguments

stat: A list of summary statistics: n (per-variant sample sizes), variantNames, and the marginal effects as z, or as b with seb.
ldReference: The LD reference the statistics' variants are matched to by stat$variantNames: a genotype panel (see readGenotypes), a GenotypeMixture or an LdMatrix. mr.ash.rss takes an LD matrix, which is formed from the reference over these variants.
varY: Variance of the phenotype, or NULL (default) to fit on the standardized scale. Used only with b and seb.
sigma2E: Initial residual variance, or NULL (default) for mr.ash.rss's own.
s0: Prior variances of the mixture components, relative to the residual variance, or NULL (default) for the grid susieR::mr.ash uses by default, built for these statistics.
w0: Prior mixture weights (summing to 1), or NULL (default) for equal weights.
fitRetention: How much of the fit is kept as the "fit" attribute of the returned weights: "none" (default) attaches nothing, "slim" and "full" attach the fitted mr.ash.rss model. This engine keeps no trimmable intermediates, so the two retaining levels behave alike here.
methodArgs: Options forwarded to susieR::mr.ash.rss, built with MrashRssOptions. A bare list is refused: it cannot be checked against the engine, so a misspelled option would be silently ignored.

Value

A numeric vector of the posterior mean of the coefficients. Unless fitRetention = "none", the fitted model is attached as attribute "fit".

Examples

data(eqtlRegionExample)
X <- eqtlRegionExample$X[, 1:30]
y <- eqtlRegionExample$yRes
ss <- lapply(seq_len(ncol(X)), function(j) {
  coef(summary(lm(y ~ X[, j])))[2, 1:2]
})
stat <- list(b = vapply(ss, `[`, numeric(1), 1L),
  seb = vapply(ss, `[`, numeric(1), 2L), n = rep(nrow(X), ncol(X)),
  variantNames = colnames(X))
mrashRssWeights(stat, LdMatrix(cor(X)))
#>                [,1]
#>  [1,] -5.579090e-08
#>  [2,] -5.579090e-08
#>  [3,]  2.834145e-08
#>  [4,] -5.120788e-09
#>  [5,] -5.120788e-09
#>  [6,] -1.862601e-08
#>  [7,] -2.598663e-08
#>  [8,]  2.898662e-08
#>  [9,] -1.433750e-08
#> [10,] -1.433750e-08
#> [11,] -7.729178e-09
#> [12,] -2.728945e-08
#> [13,] -6.958815e-09
#> [14,] -1.264231e-08
#> [15,] -7.729178e-09
#> [16,]  2.898662e-08
#> [17,] -2.496487e-08
#> [18,] -2.753271e-08
#> [19,]  2.316456e-08
#> [20,] -2.753271e-08
#> [21,] -2.753271e-08
#> [22,] -1.862601e-08
#> [23,] -2.753271e-08
#> [24,]  2.504618e-09
#> [25,] -6.958817e-09
#> [26,] -1.862602e-08
#> [27,] -7.066388e-08
#> [28,] -2.179186e-08
#> [29,]  1.263938e-08
#> [30,]  2.539543e-08