fix bug in EM 'shared_all' option

xinhe-lab · Dec 13, 2024 · a28f2d6 · a28f2d6
1 parent 82833a1
commit a28f2d6
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/R/ctwas_EM.R b/R/ctwas_EM.R
@@ -120,6 +120,7 @@ fit_EM <- function(
       tmp_EM_susie_res <- EM_susie_res[EM_susie_res$group!="SNP",]
       V_prior[names(V_prior)!="SNP"] <- sum(tmp_EM_susie_res$susie_pip*tmp_EM_susie_res$mu2)/sum(tmp_EM_susie_res$susie_pip)
     } else if (group_prior_var_structure=="shared_all") {
+      tmp_EM_susie_res <- EM_susie_res
       V_prior[names(V_prior)] <- sum(tmp_EM_susie_res$susie_pip*tmp_EM_susie_res$mu2)/sum(tmp_EM_susie_res$susie_pip)
     } else if (group_prior_var_structure=="shared_type") {
       tmp_EM_susie_res <- EM_susie_res[EM_susie_res$group=="SNP",]

diff --git a/R/ctwas_weights.R b/R/ctwas_weights.R
@@ -329,6 +329,7 @@ create_predictdb_from_QTLs <- function(weight_table,
   loginfo("Makes PredictDB weights from QTL data")
 
   # check and clean the QTL data
+  weight_table <- as.data.frame(weight_table)
   required_cols <- c("gene", "rsid", "varID", "ref_allele", "eff_allele", "weight")
   if (!all(required_cols %in% colnames(weight_table))){
     stop("QTL_data needs to contain the following columns: ",
@@ -342,7 +343,7 @@ create_predictdb_from_QTLs <- function(weight_table,
     weight_table <- weight_table[!duplicated(weight_table$gene), ]
   }
 
-  weight_table <- weight_table[weight_table[, "weight"] != 0, ,drop = FALSE]
+  weight_table <- weight_table[weight_table$weight != 0, ,drop = FALSE]
   weight_table <- weight_table[complete.cases(weight_table), ,drop = FALSE]
 
   # if NULL, create a simply extra_table based on weight_table