SuSiE-RSS Solver Settings

How the SuSiE-RSS fit is conditioned and what it falls back to, on QtlSumStats / GwasSumStats input.

SuSiE-family only, which is what the name says: every field is a susieR concept — serFallback drops to susie_ser, rFinite / rMismatch are susie_rss's R_finite / R_mismatch, and control is susie_rss_control. The other summary-statistics engine, mvsusieR::mvsusie_rss, has none of these formals and is not configured by this.

Usage

SusieRssParam(
  serFallback = FALSE,
  keepFullFit = c("fallback", "all", "none"),
  rFinite = NULL,
  rMismatch = "none",
  control = NULL
)

Arguments

serFallback

Logical. Fall back to a single-effect fit when the multi-effect fit is judged unreliable. Default FALSE.

keepFullFit

Which pre-fallback multi-effect fits to retain: "fallback" (default) keeps them only for regions that fell back, "all" for every region, "none" for none. Only meaningful when serFallback is TRUE.

rFinite

Sample size used for the LD matrix's finiteness check, or NULL (default) to use the panel's own.

rMismatch

How to treat an LD / z-score mismatch. Default "none".

control

Options for susieR::susie_rss_control(), forwarded as susie_rss()'s control argument. Built with SusieRssControlOptions; NULL (default) leaves that function's own defaults in place.

Value

A SusieRssParam object, a MethodParam.

Examples

SusieRssParam(serFallback = TRUE, keepFullFit = "all")
#> <SusieRssParam>
#>   serFallback              TRUE
#>   keepFullFit              all
#>   rMismatch                none
#>   unset: rFinite, control