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Options for Storey q-value Estimation

Source: R/qtlAssociationPostprocess.R
QvalueOptions.Rd

Build a record of extra arguments for qvalue::qvalue(), the Storey q-value engine behind qtlAssociationPostprocess.

Usage

QvalueOptions(...)

Arguments

...

Arguments for qvalue::qvalue(): pi0, the pi0.method / lambda pair that sets how the null proportion is estimated, pfdr, fdr.level and lfdr.out. qvalue()'s signature ends in ..., so names cannot be checked here and a misspelling is passed through. p is the p-value vector pecotmr assembles and is refused.

pecotmr retries qvalue() on its two documented degenerate cases ("missing or infinite" with lambda = 0, "pi0 <= 0" with a bootstrap pi0); setting lambda or pi0.method here replaces the first attempt, and the retries still override them when that attempt fails.

Value

A MethodOptions record for qtlAssociationPostprocess(qvalueArgs =).

See also

qtlAssociationPostprocess

Examples

QvalueOptions(pi0.method = "bootstrap")
#> <MethodOptions: qvalue>
#>   forwarded to qvalue::qvalue()
#>   argument names NOT checked: qvalue::qvalue() takes `...`, so any name is accepted
#>   pi0.method             bootstrap