Compute mvSuSiE-RSS TWAS weights from summary statistics

Multi-context summary-statistics analog of mvsusieWeights: extracts coefficients from an existing mvsusieR::mvsusie_rss fit, or fits one from stat$z (variants x conditions) and LD.

Usage

mvsusieRssWeights(
  stat,
  LD,
  mvsusieRssFit = NULL,
  priorVariance = NULL,
  residualVariance = NULL,
  L = 30,
  LGreedy = 5,
  retainFit = FALSE,
  ...
)

Arguments

stat

A list with z (matrix variants x conditions) and n (numeric vector or scalar).

LD

LD correlation matrix.

mvsusieRssFit

Optional pre-fitted mvsusieRss object.

priorVariance

Optional mvSuSiE prior variance specification. When NULL, mvsusieR::create_mixture_prior() is used with R = ncol(stat$z).

residualVariance

Optional residual covariance matrix.

L

Maximum number of single effects (default 30).

LGreedy

Initial greedy effect count (default 5).

retainFit

If TRUE, attaches the fitted object as an attribute.

...

Additional arguments forwarded to mvsusieR::mvsusie_rss.

Value

A numeric matrix of per-variant per-context weights (variants x conditions).

Details

Follows the *_rss_weights(stat, LD, ...) contract. Expects stat$z to be a numeric matrix (variants x conditions) and stat$n a per-context vector or scalar.