Arguments For The ctwas Fitting Steps

ctwas is not one function but nine, run in sequence, so each step's arguments travel in their own bundle and are checked against that step's own live formals — the same shape as CovUdrOptions.

This replaces a single flat bundle that was checked against the union of every step's formals. That mirrored ctwas's own ctwas_sumstats, which takes forty arguments in one signature, but it could not tell which step a name was meant for: of the 55 names in the union, 29 are accepted by exactly one step, so a name aimed at the wrong step was accepted and then silently dropped. Per-step bundles make that a construction-time error instead.

Usage

CtwasOptions(
  geneZ = CtwasGeneZOptions(),
  regionData = CtwasRegionDataOptions(),
  estParam = CtwasEstParamOptions(),
  screen = CtwasScreenOptions(),
  expand = CtwasExpandOptions(),
  finemap = CtwasFinemapOptions(),
  merge = CtwasMergeOptions(),
  boundaryGenes = CtwasBoundaryGenesOptions()
)

Arguments

geneZ

Arguments for ctwas::compute_gene_z(), built with CtwasGeneZOptions.

regionData

Arguments for ctwas::assemble_region_data(), built with CtwasRegionDataOptions.

estParam

Arguments for the group-prior EM, built with CtwasEstParamOptions.

screen

Arguments for ctwas::screen_regions(), built with CtwasScreenOptions.

expand

Arguments for ctwas::expand_region_data(), built with CtwasExpandOptions.

finemap

Arguments for ctwas::finemap_regions(), built with CtwasFinemapOptions.

merge

Arguments for the region-merging postprocess, built with CtwasMergeOptions.

boundaryGenes

Arguments for ctwas::get_boundary_genes(), built with CtwasBoundaryGenesOptions.

Value

A MethodOptions object.

Examples

CtwasOptions(
    estParam = CtwasEstParamOptions(min_group_size = 1),
    screen = CtwasScreenOptions(min_gene = 1)
)
#> <MethodOptions: ctwas>
#>   geneZ                  <S4 class 'MethodOptions' [package "pecotmr"] with 4 slots>
#>   regionData             <S4 class 'MethodOptions' [package "pecotmr"] with 4 slots>
#>   estParam               <S4 class 'MethodOptions' [package "pecotmr"] with 4 slots>
#>   screen                 <S4 class 'MethodOptions' [package "pecotmr"] with 4 slots>
#>   expand                 <S4 class 'MethodOptions' [package "pecotmr"] with 4 slots>
#>   finemap                <S4 class 'MethodOptions' [package "pecotmr"] with 4 slots>
#>   merge                  <S4 class 'MethodOptions' [package "pecotmr"] with 4 slots>
#>   boundaryGenes          <S4 class 'MethodOptions' [package "pecotmr"] with 4 slots>