Adjust SuSiE Weights — adjust_susie

Adjusts SuSiE TWAS weights by subsetting to intersected variants and optionally running allele QC against LD reference variants.

Usage

adjust_susie_weights(
  twas_weights_results,
  keep_variants,
  run_allele_qc = TRUE,
  variable_name_obj = c("susie_results", context, "variant_names"),
  susie_obj = c("susie_results", context, "susie_result_trimmed"),
  twas_weights_table = c("weights", context),
  LD_variants,
  match_min_prop = 0.2
)

Arguments

twas_weights_results: A list containing TWAS weight data (nested structure).
keep_variants: Vector of variant names to keep.
run_allele_qc: Whether to run allele_qc to align alleles. Default TRUE.
variable_name_obj: Path to variant names in the nested list.
susie_obj: Path to susie result in the nested list.
twas_weights_table: Path to weights table in the nested list.
LD_variants: Vector of LD reference variant IDs for allele QC.
match_min_prop: Minimum proportion of matched variants. Default 0.2.

Value

A list with adjusted_susie_weights and remained_variants_ids.