Renormalize Fine-Mapping PIPs to a Variant Subset

Re-derive a FineMappingEntry's PIPs (and the topLoci table) after restricting to a kept variant subset. For each effect the lbf_variable row is subset to the kept variants, renormalized via lbfToAlpha(), and the per-variant PIPs are recomputed as 1 - prod_l(1 - alpha[l, p]).

The two scenarios this supports:

• The user declined to impute missing variants in a GWAS SumStats, so a downstream fine-mapping result needs PIPs restricted to the GWAS-covered intersection.

• Colocalization between a GWAS FineMappingResult and a QTL FineMappingResult computed on different variant sets — the GWAS PIPs (or QTL PIPs) get renormalized to the common variant set.

Usage

adjustPips(x, keepVariants, ...)

# S4 method for class 'FineMappingResultBase'
adjustPips(x, keepVariants, ...)

# S4 method for class 'FineMappingEntry'
adjustPips(x, keepVariants, ...)

Arguments

x

A FineMappingEntry or FineMappingResultBase.

keepVariants

Character vector of variant IDs to keep. Intersected with the entry's own variantIds; an empty intersection raises an error.

...

Future expansion.

Value

The same flavour of object with PIPs renormalized on the kept subset.