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fix variant name mismatch 'chr' #428

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Merged
gaow merged 1 commit into from
Jan 6, 2026
Merged

fix variant name mismatch 'chr' #428

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11 changes: 6 additions & 5 deletions R/twas.R
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Original file line number Diff line number Diff line change
Expand Up @@ -172,8 +172,8 @@ harmonize_twas <- function(twas_weights_data, ld_meta_file_path, gwas_meta_file,
rownames(weights_matrix_subset) <- weights_matrix_qced$target_data_qced$variant_id # weight variant names are flipped/corrected

# intersect post-qc gwas and post-qc weight variants
gwas_LD_variants <- intersect(gwas_data_sumstats$variant_id, LD_list$combined_LD_variants)
weights_matrix_subset <- weights_matrix_subset[rownames(weights_matrix_subset) %in% gwas_LD_variants, , drop = FALSE]
gwas_LD_variants <- intersect(gsub("chr","", gwas_data_sumstats$variant_id), gsub("chr","", LD_list$combined_LD_variants))
weights_matrix_subset <- weights_matrix_subset[rownames(weights_matrix_subset) %in% gsub("chr","", gwas_data_sumstats$variant_id), , drop = FALSE]
if (nrow(weights_matrix_subset) == 0) next
postqc_weight_variants <- rownames(weights_matrix_subset)

Expand Down Expand Up @@ -222,7 +222,7 @@ harmonize_twas <- function(twas_weights_data, ld_meta_file_path, gwas_meta_file,
results[[molecular_id]][["weights_qced"]][[context]][[study]] <- list(scaled_weights = weights_matrix_subset * sqrt(variance), weights = weights_matrix_subset)
}
# Combine gwas sumstat across different context for a single context group based on all variants included in this molecular_id/gene/region
gwas_data_sumstats$variant_id <- paste0("chr", gwas_data_sumstats$variant_id)
gwas_data_sumstats$variant_id <- ifelse(startsWith(gwas_data_sumstats$variant_id, "chr"), gwas_data_sumstats$variant_id, paste0("chr", gwas_data_sumstats$variant_id))
gwas_data_sumstats <- gwas_data_sumstats[gwas_data_sumstats$variant_id %in% unique(find_data(results[[molecular_id]][["variant_names"]], c(2, study))), , drop = FALSE]
results[[molecular_id]][["gwas_qced"]][[study]] <- rbind(results[[molecular_id]][["gwas_qced"]][[study]], gwas_data_sumstats)
results[[molecular_id]][["gwas_qced"]][[study]] <- results[[molecular_id]][["gwas_qced"]][[study]][!duplicated(results[[molecular_id]][["gwas_qced"]][[study]][, c("variant_id", "z")]), ]
Expand All @@ -234,9 +234,10 @@ harmonize_twas <- function(twas_weights_data, ld_meta_file_path, gwas_meta_file,
if (is.null(all_molecular_variants)) {
results[[molecular_id]] <- NULL
} else {
var_indx <- match(all_molecular_variants, paste0("chr", LD_list$combined_LD_variants))
var_indx <- match(all_molecular_variants, ifelse(startsWith(LD_list$combined_LD_variants, "chr"), LD_list$combined_LD_variants, paste0("chr", LD_list$combined_LD_variants)))
results[[molecular_id]][["LD"]] <- as.matrix(LD_list$combined_LD_matrix[var_indx, var_indx])
rownames(results[[molecular_id]][["LD"]]) <- colnames(results[[molecular_id]][["LD"]]) <- paste0("chr", colnames(results[[molecular_id]][["LD"]]))
rownames(results[[molecular_id]][["LD"]]) <- colnames(results[[molecular_id]][["LD"]]) <- ifelse(startsWith(colnames(results[[molecular_id]][["LD"]]), "chr"),
colnames(results[[molecular_id]][["LD"]]), paste0("chr", colnames(results[[molecular_id]][["LD"]])))
}
}
# return results
Expand Down
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