add log file

DESCRIPTION

@@ -4,7 +4,7 @@ Type: Package
 Title: Adjusting for Genetic Confounders in Transcriptome-Wide Association
   Studies Improves Discovery of Risk Genes of Complex Traits
 Date: 2024-06-14
-Version: 0.3.10
+Version: 0.3.11
 Authors@R: c(person("Siming","Zhao",role="aut",email="siming.zhao06@gmail.com"),
              person("Wesley","Crouse",role="aut"),
              person("Sheng","Qian",role="aut",email="shengqian@uchicago.edu"),

R/ctwas_merge_regions.R

@@ -69,9 +69,12 @@ merge_region_data <- function(boundary_genes,
                               logfile = NULL,
                               ...) {
 
-  # Identify overlapping regions and get a list of regions to be merged
-  loginfo("Identify overlapping regions and get region_info for merged regions.")
+  if (!is.null(logfile)){
+    addHandler(writeToFile, file= logfile, level='DEBUG')
+  }
 
+  # Identify overlapping regions and get a list of regions to be merged
+  loginfo("Identify overlapping regions and create merged snp_map and LD_map.")
   res <- create_merged_snp_LD_map(boundary_genes,
                                   region_info = region_info,
                                   snp_map = snp_map,

R/ctwas_utils.R

@@ -217,7 +217,6 @@ read_var_info <- function(var_info_file){
 
 # run mclapply and stop if not all cores delivered results
 mclapply_check <- function(X, FUN, mc.cores = 1){
-
   if (length(X) <= 1 || mc.cores == 1) {
     lapply(X, FUN)
   } else {
@@ -229,13 +228,6 @@ mclapply_check <- function(X, FUN, mc.cores = 1){
     }
     )
   }
-
 }
 
-# # check mclapply result
-# check_mc_res <- function(x){
-#   if (any(sapply(x, is.null))) {
-#     stop("Not all cores returned results. Try rerun with bigger memory or fewer cores")
-#   }
-# }