add warning message for duplicated names of region_data

Author: kevinlkx

R/ctwas_est_parameters.R

@@ -34,7 +34,7 @@
 #'
 #' @param ... Additional arguments of \code{susie_rss}.
 #'
-#' @importFrom logging addHandler loginfo writeToFile
+#' @importFrom logging addHandler loginfo logwarn writeToFile
 #'
 #' @return a list with estimated parameters
 #'
@@ -65,9 +65,11 @@ est_param <- function(
   # check inputs
   group_prior_var_structure <- match.arg(group_prior_var_structure)
 
-  if (!inherits(region_data,"list")){
+  if (!inherits(region_data,"list"))
     stop("'region_data' should be a list.")
-  }
+
+  if (anyDuplicated(names(region_data)))
+    logwarn("Duplicated names of region_data found! Please use unique names for region_data!")
 
   # extract thin value from region_data
   thin <- unique(sapply(region_data, "[[", "thin"))
@@ -103,16 +105,16 @@ est_param <- function(
     skip_region_ids <- region_ids[(n_sids + n_gids) < min_var]
     if (length(skip_region_ids) > 0){
       loginfo("Skip %d regions with number of variables < %d.", length(skip_region_ids), min_var)
-      region_data[skip_region_ids] <- NULL
+      region_data <- region_data[!names(region_data) %in% skip_region_ids]
     }
   }
 
   # skip regions with fewer than min_gene genes
   if (min_gene > 0) {
     skip_region_ids <- region_ids[n_gids < min_gene]
     if (length(skip_region_ids) > 0){
-      loginfo("Remove %d regions with number of genes < %d.", length(skip_region_ids), min_gene)
-      region_data[skip_region_ids] <- NULL
+      loginfo("Skip %d regions with number of genes < %d.", length(skip_region_ids), min_gene)
+      region_data <- region_data[!names(region_data) %in% skip_region_ids]
     }
   }
 

R/ctwas_finemapping.R

@@ -90,6 +90,9 @@ finemap_regions <- function(region_data,
   if (!inherits(region_data,"list"))
     stop("'region_data' should be a list.")
 
+  if (anyDuplicated(names(region_data)))
+    logwarn("Duplicated names of region_data found! Please use unique names for region_data!")
+
   if (missing(LD_map))
     stop("'LD_map' is required when running with LD!")
 
@@ -130,7 +133,6 @@ finemap_regions <- function(region_data,
   }
 
   region_ids <- names(region_data)
-
   res <- mclapply_check(region_ids, function(region_id){
     finemap_single_region(region_data = region_data,
                           region_id = region_id,
@@ -196,7 +198,7 @@ finemap_regions <- function(region_data,
 #'
 #' @return a data frame of cTWAS finemapping results.
 #'
-#' @importFrom logging addHandler loginfo writeToFile
+#' @importFrom logging addHandler loginfo logwarn writeToFile
 #' @importFrom parallel mclapply
 #'
 #' @export
@@ -221,6 +223,9 @@ finemap_regions_noLD <- function(region_data,
   if (!inherits(region_data,"list"))
     stop("'region_data' should be a list!")
 
+  if (anyDuplicated(names(region_data)))
+    logwarn("Duplicated names of region_data found! Please use unique names for region_data!")
+
   if (verbose) {
     if (is.null(group_prior)) {
       loginfo("Use uniform prior.")
@@ -231,7 +236,6 @@ finemap_regions_noLD <- function(region_data,
   }
 
   region_ids <- names(region_data)
-
   res <- mclapply_check(region_ids, function(region_id){
     finemap_single_region_noLD(region_data = region_data,
                                region_id = region_id,
@@ -592,7 +596,8 @@ fast_finemap_single_region_L1_noLD <- function(region_data,
   rm(regiondata)
 
   if (length(z) < 2) {
-    stop(paste(length(z), "variables in the region. At least two variables in a region are needed to run susie"))
+    stop(paste(length(z), "variables in the region", region_id, "\n",
+               "At least two variables in a region are needed to run susie"))
   }
 
   # update priors, prior variances and null_weight

R/ctwas_screen_regions.R

@@ -232,7 +232,7 @@ screen_regions <- function(region_data,
 #' @return a list, containing a data frame of selected region data,
 #' and a data frame of screening summary for all regions.
 #'
-#' @importFrom logging addHandler loginfo writeToFile
+#' @importFrom logging addHandler loginfo logwarn writeToFile
 #'
 #' @export
 #'
@@ -267,13 +267,17 @@ screen_regions_noLD <- function(region_data,
   if (!inherits(region_data,"list"))
     stop("'region_data' should be a list.")
 
+  if (anyDuplicated(names(region_data)))
+    logwarn("Duplicated names of region_data found! Please use unique names for region_data!")
+
   # adjust group_prior to account for thin argument
   if (!is.null(group_prior)){
     group_prior["SNP"] <- group_prior["SNP"]/thin
   }
 
   # create a data frame for screening summary
   region_ids <- names(region_data)
+
   n_gids <- sapply(region_data, function(x){length(x$gid)})
   n_sids <- sapply(region_data, function(x){length(x$sid)})
   screen_summary <- data.frame(region_id = region_ids,
@@ -287,16 +291,16 @@ screen_regions_noLD <- function(region_data,
     skip_region_ids <- region_ids[(n_sids + n_gids) < min_var]
     if (length(skip_region_ids) > 0){
       loginfo("Skip %d regions with number of variables < %d.", length(skip_region_ids), min_var)
-      region_data[skip_region_ids] <- NULL
+      region_data <- region_data[!names(region_data) %in% skip_region_ids]
     }
   }
 
   # skip regions with fewer than min_gene genes
   if (min_gene > 0) {
     skip_region_ids <- region_ids[n_gids < min_gene]
     if (length(skip_region_ids) > 0){
-      loginfo("Remove %d regions with number of genes < %d.", length(skip_region_ids), min_gene)
-      region_data[skip_region_ids] <- NULL
+      loginfo("Skip %d regions with number of genes < %d.", length(skip_region_ids), min_gene)
+      region_data <- region_data[!names(region_data) %in% skip_region_ids]
     }
   }