Arguments For A Fine-Mapping Engine

Options forwarded to one fine-mapping engine, checked against that engine's live formals.

There is one constructor per ENGINE, not per method. A method whose individual-level and summary-statistic paths run different functions has one for each — SusieOptions for susieR::susie and SusieRssOptions for susieR::susie_rss, MvsusieOptions and MvsusieRssOptions likewise. Checking the union of the two instead would accept an susie_rss-only name on an individual-level run and then silently drop it, and would leave mvsusie unchecked entirely, since mvsusie_rss takes ... and a union containing it accepts any name at all.

SerOptions and FsusieOptions have no sibling: SER is summary-statistics-only and fSuSiE individual-only.

Pass the result as an element of FineMappingMethodsParam, or directly to the matching single-engine function. In the aggregator a method accepts either of its engines' constructors, since the input class is not known at that point. A plain list works there too and stays checked against both; the exact engine is checked once the run's input class is known.

Usage

SusieOptions(...)

SusieRssOptions(...)

SusieInfOptions(...)

SusieInfRssOptions(...)

SusieAshOptions(...)

SusieAshRssOptions(...)

SerOptions(...)

MvsusieOptions(...)

MvsusieRssOptions(...)

FsusieOptions(...)

Arguments

...

Arguments for the engine, under its own names (L, coverage, max_iter, ...).

Value

A MethodOptions object.

Examples

SusieOptions(max_iter = 200)
#> <MethodOptions: susie>
#>   forwarded to susieR::susie()
#>   argument names checked against susieR::susie()
#>   for input class QtlDataset
#>   max_iter               200
SusieRssOptions(maf_thresh = 0.01)
#> <MethodOptions: susieRss>
#>   forwarded to susieR::susie_rss()
#>   argument names checked against susieR::susie_rss()
#>   for input class GwasSumStats, QtlSumStats
#>   maf_thresh             0.01
MvsusieOptions(prior_tol = 1e-9)
#> <MethodOptions: mvsusie>
#>   forwarded to mvsusieR::mvsusie()
#>   argument names checked against mvsusieR::mvsusie()
#>   for input class QtlDataset
#>   prior_tol              1e-09