Fine-mapping with SuSiE

The summary data method extensions of the SuSiE model (implemented in the susieR R package) can be used with LD reference panels to identify causal genetic variants from GWAS or QTL summary statistics.

library(bedrockbio)
library(susieR)

pqtls <- load_dataset("ukb_ppp/pqtls") |>
    filter(
        ancestry == "EUR",
        protein == "P43220"
    ) |>
    select(
        chromosome,
        position,
        effect_allele,
        other_allele,
        beta,
        standard_error
    )

ld <- load_dataset("pan_ukbb/ld/matrix") |>
    filter(
        ancestry == "EUR"
    ) |>
    semi_join(
        pqtls,
        by=c("chromosome", "position_i" = "position")
    )