Which Fine-Mapping Methods To Run, And How — FineMappingMethodsParam-class • pecotmr

Selects the methods fineMappingPipeline runs and carries each one's engine arguments.

A method that runs on both individual-level and summary-statistic data reaches a different engine on each path, so for a MultiStudyQtlDataset carrying both there is no single set of arguments per method. Name such a method under qtlDatasetMethods or qtlSumStatsMethods to say which path its options are for; name it under methods when the path need not be stated — a single-type run, or a method with nothing path-specific to configure.

Naming a method selects it. A method belongs in exactly one of the three slots.

Usage

FineMappingMethodsParam(
  methods = NULL,
  qtlDatasetMethods = NULL,
  qtlSumStatsMethods = NULL
)

Arguments

methods: Named list of per-method options whose input path need not be stated. Each entry is that method's *Options() record, or list() to run it with its defaults.
qtlDatasetMethods: Named list of per-method options for the individual-level path.
qtlSumStatsMethods: Named list of per-method options for the summary-statistics path.

Value

A FineMappingMethodsParam object, a MethodParam.

Examples

FineMappingMethodsParam(methods = "susie")
#> <FineMappingMethodsParam>
#>   methods                  susie
#>   unset: qtlDatasetMethods, qtlSumStatsMethods
FineMappingMethodsParam(
  methods = list(susie = SusieOptions(max_iter = 200))
)
#> <FineMappingMethodsParam>
#>   methods                  susie
#>   unset: qtlDatasetMethods, qtlSumStatsMethods
FineMappingMethodsParam(
    qtlDatasetMethods = list(susie = SusieOptions(max_iter = 200)),
    qtlSumStatsMethods = list(susie = SusieRssOptions(max_iter = 200))
)
#> <FineMappingMethodsParam>
#>   qtlDatasetMethods        susie
#>   qtlSumStatsMethods       susie
#>   unset: methods