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update maximum snp number restriction #389

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Merged
gaow merged 1 commit into from
May 16, 2025
Merged

update maximum snp number restriction #389

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11 changes: 5 additions & 6 deletions R/ctwas_wrapper.R
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Original file line number Diff line number Diff line change
Expand Up @@ -68,12 +68,11 @@ trim_ctwas_variants <- function(region_data, twas_weight_cutoff = 1e-5, cs_min_c
high_pip_variants <- names(context_pip[context_pip > min_pip_cutoff])[names(context_pip[context_pip > min_pip_cutoff]) %in% rownames(weight_list$wgt)]
selected_variants_by_context <- unique(c(selected_variants_by_context, high_pip_variants))

if (length(selected_variants_by_context) < max_num_variants) {
remaining_var_num <- max_num_variants - length(selected_variants_by_context)
available_variants <- setdiff(names(context_pip)[names(context_pip) %in% rownames(weight_list$wgt)], selected_variants_by_context)
context_pip <- context_pip[available_variants]
selected_variants_by_context <- c(selected_variants_by_context, names(context_pip[order(-context_pip)])[1:remaining_var_num])
}
# prioritize SNPs based on PIP if max_num_variants different from Inf
available_variants <- intersect(rownames(weight_list$wgt), names(context_pip))
prioritized <- unique(c(selected_variants_by_context, setdiff(available_variants, selected_variants_by_context)))
prioritized <- prioritized[order(-context_pip[prioritized])]
selected_variants_by_context <- head(prioritized, max_num_variants)
weight_list$wgt <- weight_list$wgt[selected_variants_by_context, , drop = FALSE]
return(weight_list)
}
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