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modication of quantile twas #376

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Merged
gaow merged 1 commit into from
Apr 11, 2025
Merged

modication of quantile twas #376

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43 changes: 32 additions & 11 deletions R/twas.R
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Original file line number Diff line number Diff line change
Expand Up @@ -486,6 +486,9 @@ twas_pipeline <- function(twas_weights_data,
twas_data_qced[[weight_db]][["weights_qced"]][[context]][[study]][["weights"]], twas_data_qced[[weight_db]][["gwas_qced"]][[study]],
twas_data_qced[[weight_db]][["LD"]], twas_variants
)
if (is.null(twas_rs)) {
return(list(twas_rs_df = data.frame(), mr_rs_df = data.frame()))
}
twas_rs_df <- data.frame(
gwas_study = study, method = sub("_[^_]+$", "", names(twas_rs)), twas_z = find_data(twas_rs, c(2, "z")),
twas_pval = find_data(twas_rs, c(2, "pval")), context = context, molecular_id = weight_db
Expand Down Expand Up @@ -545,17 +548,32 @@ twas_pipeline <- function(twas_weights_data,
gene_table <- do.call(rbind, lapply(contexts, function(context) {
methods <- sub("_[^_]+$", "", names(twas_weights_data[[molecular_id]]$twas_cv_performance[[context]]))
if (quantile_twas) {
# Quantile TWAS data extraction
quantile_starts <- sapply(twas_weights_data[[molecular_id]]$twas_cv_performance[[context]], function(x) x[, "quantile_start"])
quantile_ends <- sapply(twas_weights_data[[molecular_id]]$twas_cv_performance[[context]], function(x) x[, "quantile_end"])
pseudo_R2_avgs <- sapply(twas_weights_data[[molecular_id]]$twas_cv_performance[[context]], function(x) x[, "pseudo_R2_avg"])

context_table <- data.frame(
context = context, method = methods,
quantile_start = quantile_starts, quantile_end = quantile_ends,
pseudo_R2_avg = pseudo_R2_avgs,
type = twas_weights_data[[molecular_id]][["data_type"]][[context]]
)
cv_performance <- twas_weights_data[[molecular_id]]$twas_cv_performance[[context]]
if (length(methods) == 0) {
context_table <- data.frame()
} else {
method_results <- list()

for (method in methods) {
if (!is.null(cv_performance[[paste0(method, "_performance")]])) {
performance_data <- cv_performance[[paste0(method, "_performance")]]
method_results[[method]] <- data.frame(
context = context,
method = method,
quantile_start = performance_data[, "quantile_start"],
quantile_end = performance_data[, "quantile_end"],
pseudo_R2_avg = performance_data[, "pseudo_R2_avg"],
type = twas_weights_data[[molecular_id]][["data_type"]][[context]]
)
}
}

if (length(method_results) > 0) {
context_table <- do.call(rbind, method_results)
} else {
context_table <- data.frame()
}
}
} else {
# Original TWAS data extraction
is_imputable <- twas_data[[molecular_id]][["model_selection"]][[context]]$is_imputable
Expand Down Expand Up @@ -588,6 +606,9 @@ twas_pipeline <- function(twas_weights_data,
} else {
c("chr", "molecular_id", "context", "gwas_study", "method", "is_imputable", "is_selected_method", "rsq_cv", "pval_cv", "twas_z", "twas_pval", "type", "block")
}
if (nrow(twas_results_table) == 0) {
return(list(twas_result = NULL, twas_data = NULL, mr_result = NULL))
}
twas_table <- merge(twas_table, twas_results_table, by = c("molecular_id", "context", "method"))
if (!quantile_twas) {
twas_table <- twas_table[twas_table$is_imputable, , drop = FALSE]
Expand Down
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